From owner-rapd@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!umn.edu!gaia.ucs.orst.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Operon primer sequences Message-ID: <265m8i$bpd@news.u.washington.edu> Date: 2 Sep 93 20:49:22 GMT Organization: University of Washington, Seattle Lines: 9 NNTP-Posting-Host: stein.u.washington.edu Has anybody keyed in the Operon primer sequences along with their Operon names? We could use this list on our Populus mapping database, but don't want to type it in ourselves. Toby Bradshaw | Department of Biochemistry | Will make genetic linkage maps and College of Forest Resources | for food. University of Washington, Seattle | toby@u.washington.edu | From owner-rapd@net.bio.net Fri Sep 03 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!math.ohio-state.edu!news.acns.nwu.edu!raven.alaska.edu!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Operon primers to be on-line Message-ID: <268mpu$6t8@news.u.washington.edu> Date: 4 Sep 93 00:17:02 GMT Organization: University of Washington, Seattle Lines: 11 NNTP-Posting-Host: stein.u.washington.edu The good folks at Operon have their primer sequences available as an ASCII file on diskette for $15. After some dedicated wheedling I obtained permission to distribute this information if I buy the diskette. So, when the diskette comes in I'll post the sequences to this newsgroup and place the file on the Poplar Molecular Network anonymous ftp site (gopher-able at: poplar1.cfr.washington.edu). Thanks to Antoni Rafalski who suggested this approach. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Sun Sep 05 23:00:00 1993 Path: biosci!CABELL.VCU.EDU!blbrown From: blbrown@CABELL.VCU.EDU (Bonnie L. Brown) Newsgroups: bionet.molbio.rapd Subject: primer/temp studies Message-ID: <9309061537.AA04987@cabell.vcu.edu> Date: 6 Sep 93 15:37:37 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Has anyone done/seen published any studies concerning the primer-dependent production of high molecular weight bands and /or smears using RAPD/PCR? We are specifically interested in the relation of high molecular weight band production and annealing temperature. BLBrown Biology Dept. Virginia Commonwealth Univ. Richmond, VA 23284 blbrown@cabell.vcu.edu From owner-rapd@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!julienas!jouy!jouy!bertheau From: bertheau@jouy.jouy.inra.fr (Yves Bertheau) Newsgroups: bionet.molbio.rapd Subject: Re: AFLP Info Message-ID: <1993Sep8.083416.25241@inra.fr> Date: 8 Sep 93 08:34:16 GMT References: Sender: news@inra.fr Organization: INRA Lines: 48 Nntp-Posting-Host: jouy X-Newsreader: Tin 1.1 PL4 pveck@rcl.wau.nl writes: : In article , mcclean@plains (Phillip McClean) writes: : >I recently became aware of AFLPs. Does anyone have any info to share : >regarding this technology? : > : >Phil McClean : >North Dakota State University : >mcclean@plains.nodak.edu : : Yes, I do know about AFLP, although I do not know whether we mean the same : technique. AFLP, Amplified Fragm.Length Polymorphism is a technique : developed : by a company called KeyGene, SciencePark, Wageningen, The Netherlands : It combines the best of a PCR based technique with the reproduciblity of : RFLPs. The technique is patented, and will be commercialized in a kit. : : Outline: 4 : Restriction digestion : Sticky end ligation with 'adaptor' : annealing with primer which is basepairing with : the adaptor and the restriction site and two or three extra : nucleotides. : This is a selective step, because only a few of all : restriction fragments will be compatible with the : primer. : PCR : separation. : : I'm leaving out details which are not necessairy to understand the : principle. The results are amazing. Reproducible patterns which : monitor about 100 loci simultaneously. : : Herman van Eck Hi, Does anybody know the address of the KEYGENE company with its fax number? Moreover, are the papers concerning AFLPs been published and the kits yet selled by this company? Thanks in advance Yves Bertheau bertheau@inapv.inapg.inra.fr -- Yves Bertheau INRA, Pathologie Vegetale, 16 rue Claude Bernard, 75231 Paris cedex 05, FRANCE. bertheau@inapv.inapg.inra.fr Tel +33 (1) 44.08.17.04 Fax: +33 (1) 44.08.17.00 From owner-rapd@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: URA3/FOA positive/neg selection in other yeasts. Message-ID: <439479042C2@uamercury.uark.edu> Date: 8 Sep 93 16:51:59 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 19 >Date: Wed, 08 Sep 93 08:57:54 EDT >From: FOF%FDACFSAN.BITNET@net.bio.net >To: YEAST@net.bio.net >Subject: URA3/FOA positive/neg selection in other yeasts. >Does anyone know whether Boeke and Fink's URA3/FOA positive/negative selection >has been used in yeasts other than S. cer.? How about Nancy Kleckner's >method of removing URA3 by flanking it with hisG repeats? The approach was not `completely' utilized but should be possible given the data presented in a paper by Kelley, Miller, Kurtz and Kirsch in Mole Cell Biol 7(1):199-207. There work was with a URA3 disruption with an ADE2 disruption cassette in Candida albicans. The disruption was 5FOA sensitive so that the system should be utilizable with a complete URA3 disruption strain. Doug Rhoads || Dept. of Biological Sciences drhoads@mercury.uark.edu || 601 Science Engineering drhoads@uafsysb.uark.edu || University of Arkansas 501-575-3251 || Fayetteville, AR 72701 From owner-rapd@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!psgrain!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!brknig01 From: brknig01@uctvax.uct.ac.za Newsgroups: bionet.molbio.rapd Subject: radp on crop grasses Summary: rapd, sorghum, crop grasses Keywords: rapd sorghum bicolor, crop grasses Message-ID: <1993Sep8.115154.205014@uctvax.uct.ac.za> Date: 8 Sep 93 09:51:54 GMT Reply-To: nigel@chempath.uct.ac.za Organization: University of Cape Town Lines: 9 Hi netters A colleague of mine from Zimbabwe wishes to know if any of you have applied the rapd technique to cultivated crop grasses, in particular Sorghum bicolor Please reply to me at Nigel@chempath.uct.ac.za Thanks! Nigel Barker From owner-rapd@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Keygene Message-ID: <9309081229.AA13300@esds01.es.dupont.com> Date: 8 Sep 93 12:29:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 In response to a question about Keygene from Yves Bertheau bertheau@inapv.inapg.inra.fr : Keygene n.v. Dr. Marc Zabeau, General Manager Agro Business Park 90 POBox 216, 6700 AE Wageningen The Netherlands Tel 31 8370 24141 fax 31 8370 24939 There is a short publication (Smith Zabeau and Wright) on the Keygene technology (AFLPs) in Maize Genetics Newsletter #67 (March 1993) p.62-64. Also, the European patent application is available (quite detailed) : European Patent Office publication # 0 534 858 A1 (Application number 92402629.7, filed Sept. 24, 1992. Antoni Rafalski From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!zaphod.crihan.fr!univ-lyon1.fr!ghost.dsi.unimi.it!batcomputer!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!stein1.u.washington.edu!toby From: toby@stein1.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Operon Technologies, Inc. 10-mer names/sequences Message-ID: <26nocb$omb@news.u.washington.edu> Date: 9 Sep 93 17:15:55 GMT Organization: University of Washington, Seattle Lines: 1007 NNTP-Posting-Host: stein.u.washington.edu The following is a list of Operon Technologies, Inc. primer names and sequences, provided by Operon and available for distribution to interested parties. The list will be available soon by anonymous ftp or gopher from the Poplar Molecular Network at poplar1.cfr.washington.edu. " A-01","CAGGCCCTTC" " A-02","TGCCGAGCTG" " A-03","AGTCAGCCAC" " A-04","AATCGGGCTG" " A-05","AGGGGTCTTG" " A-06","GGTCCCTGAC" " A-07","GAAACGGGTG" " A-08","GTGACGTAGG" " A-09","GGGTAACGCC" " A-10","GTGATCGCAG" " A-11","CAATCGCCGT" " A-12","TCGGCGATAG" " A-13","CAGCACCCAC" " A-14","TCTGTGCTGG" " A-15","TTCCGAACCC" " A-16","AGCCAGCGAA" " A-17","GACCGCTTGT" " A-18","AGGTGACCGT" " A-19","CAAACGTCGG" " A-20","GTTGCGATCC" " B-01","GTTTCGCTCC" " B-02","TGATCCCTGG" " B-03","CATCCCCCTG" " B-04","GGACTGGAGT" " B-05","TGCGCCCTTC" " B-06","TGCTCTGCCC" " B-07","GGTGACGCAG" " B-08","GTCCACACGG" " B-09","TGGGGGACTC" " B-10","CTGCTGGGAC" " B-11","GTAGACCCGT" " B-12","CCTTGACGCA" " B-13","TTCCCCCGCT" " B-14","TCCGCTCTGG" " B-15","GGAGGGTGTT" " B-16","TTTGCCCGGA" " B-17","AGGGAACGAG" " B-18","CCACAGCAGT" " B-19","ACCCCCGAAG" " B-20","GGACCCTTAC" " C-01","TTCGAGCCAG" " C-02","GTGAGGCGTC" " C-03","GGGGGTCTTT" " C-04","CCGCATCTAC" " C-05","GATGACCGCC" " C-06","GAACGGACTC" " C-07","GTCCCGACGA" " C-08","TGGACCGGTG" " C-09","CTCACCGTCC" " C-10","TGTCTGGGTG" " C-11","AAAGCTGCGG" " C-12","TGTCATCCCC" " C-13","AAGCCTCGTC" " C-14","TGCGTGCTTG" " C-15","GACGGATCAG" " C-16","CACACTCCAG" " C-17","TTCCCCCCAG" " C-18","TGAGTGGGTG" " C-19","GTTGCCAGCC" " C-20","ACTTCGCCAC" " D-01","ACCGCGAAGG" " D-02","GGACCCAACC" " D-03","GTCGCCGTCA" " D-04","TCTGGTGAGG" " D-05","TGAGCGGACA" " D-06","ACCTGAACGG" " D-07","TTGGCACGGG" " D-08","GTGTGCCCCA" " D-09","CTCTGGAGAC" " D-10","GGTCTACACC" " D-11","AGCGCCATTG" " D-12","CACCGTATCC" " D-13","GGGGTGACGA" " D-14","CTTCCCCAAG" " D-15","CATCCGTGCT" " D-16","AGGGCGTAAG" " D-17","TTTCCCACGG" " D-18","GAGAGCCAAC" " D-19","CTGGGGACTT" " D-20","ACCCGGTCAC" " E-01","CCCAAGGTCC" " E-02","GGTGCGGGAA" " E-03","CCAGATGCAC" " E-04","GTGACATGCC" " E-05","TCAGGGAGGT" " E-06","AAGACCCCTC" " E-07","AGATGCAGCC" " E-08","TCACCACGGT" " E-09","CTTCACCCGA" " E-10","CACCAGGTGA" " E-11","GAGTCTCAGG" " E-12","TTATCGCCCC" " E-13","CCCGATTCGG" " E-14","TGCGGCTGAG" " E-15","ACGCACAACC" " E-16","GGTGACTGTG" " E-17","CTACTGCCGT" " E-18","GGACTGCAGA" " E-19","ACGGCGTATG" " E-20","AACGGTGACC" " F-01","ACGGATCCTG" " F-02","GAGGATCCCT" " F-03","CCTGATCACC" " F-04","GGTGATCAGG" " F-05","CCGAATTCCC" " F-06","GGGAATTCGG" " F-07","CCGATATCCC" " F-08","GGGATATCGG" " F-09","CCAAGCTTCC" " F-10","GGAAGCTTGG" " F-11","TTGGTACCCC" " F-12","ACGGTACCAG" " F-13","GGCTGCAGAA" " F-14","TGCTGCAGGT" " F-15","CCAGTACTCC" " F-16","GGAGTACTGG" " F-17","AACCCGGGAA" " F-18","TTCCCGGGTT" " F-19","CCTCTAGACC" " F-20","GGTCTAGAGG" " G-01","CTACGGAGGA" " G-02","GGCACTGAGG" " G-03","GAGCCCTCCA" " G-04","AGCGTGTCTG" " G-05","CTGAGACGGA" " G-06","GTGCCTAACC" " G-07","GAACCTGCGG" " G-08","TCACGTCCAC" " G-09","CTGACGTCAC" " G-10","AGGGCCGTCT" " G-11","TGCCCGTCGT" " G-12","CAGCTCACGA" " G-13","CTCTCCGCCA" " G-14","GGATGAGACC" " G-15","ACTGGGACTC" " G-16","AGCGTCCTCC" " G-17","ACGACCGACA" " G-18","GGCTCATGTG" " G-19","GTCAGGGCAA" " G-20","TCTCCCTCAG" " H-01","GGTCGGAGAA" " H-02","TCGGACGTGA" " H-03","AGACGTCCAC" " H-04","GGAAGTCGCC" " H-05","AGTCGTCCCC" " H-06","ACGCATCGCA" " H-07","CTGCATCGTG" " H-08","GAAACACCCC" " H-09","TGTAGCTGGG" " H-10","CCTACGTCAG" " H-11","CTTCCGCAGT" " H-12","ACGCGCATGT" " H-13","GACGCCACAC" " H-14","ACCAGGTTGG" " H-15","AATGGCGCAG" " H-16","TCTCAGCTGG" " H-17","CACTCTCCTC" " H-18","GAATCGGCCA" " H-19","CTGACCAGCC" " H-20","GGGAGACATC" " I-01","ACCTGGACAC" " I-02","GGAGGAGAGG" " I-03","CAGAAGCCCA" " I-04","CCGCCTAGTC" " I-05","TGTTCCACGG" " I-06","AAGGCGGCAG" " I-07","CAGCGACAAG" " I-08","TTTGCCCGGT" " I-09","TGGAGAGCAG" " I-10","ACAACGCGAG" " I-11","ACATGCCGTG" " I-12","AGAGGGCACA" " I-13","CTGGGGCTGA" " I-14","TGACGGCGGT" " I-15","TCATCCGAGG" " I-16","TCTCCGCCCT" " I-17","GGTGGTGATG" " I-18","TGCCCAGCCT" " I-19","AATGCGGGAG" " I-20","AAAGTGCGGG" " J-01","CCCGGCATAA" " J-02","CCCGTTGGGA" " J-03","TCTCCGCTTG" " J-04","CCGAACACGG" " J-05","CTCCATGGGG" " J-06","TCGTTCCGCA" " J-07","CCTCTCGACA" " J-08","CATACCGTGG" " J-09","TGAGCCTCAC" " J-10","AAGCCCGAGG" " J-11","ACTCCTGCGA" " J-12","GTCCCGTGGT" " J-13","CCACACTACC" " J-14","CACCCGGATG" " J-15","TGTAGCAGGG" " J-16","CTGCTTAGGG" " J-17","ACGCCAGTTC" " J-18","TGGTCGCAGA" " J-19","GGACACCACT" " J-20","AAGCGGCCTC" " K-01","CATTCGAGCC" " K-02","GTCTCCGCAA" " K-03","CCAGCTTAGG" " K-04","CCGCCCAAAC" " K-05","TCTGTCGAGG" " K-06","CACCTTTCCC" " K-07","AGCGAGCAAG" " K-08","GAACACTGGG" " K-09","CCCTACCGAC" " K-10","GTGCAACGTG" " K-11","AATGCCCCAG" " K-12","TGGCCCTCAC" " K-13","GGTTGTACCC" " K-14","CCCGCTACAC" " K-15","CTCCTGCCAA" " K-16","GAGCGTCGAA" " K-17","CCCAGCTGTG" " K-18","CCTAGTCGAG" " K-19","CACAGGCGGA" " K-20","GTGTCGCGAG" " L-01","GGCATGACCT" " L-02","TGGGCGTCAA" " L-03","CCAGCAGCTT" " L-04","GACTGCACAC" " L-05","ACGCAGGCAC" " L-06","GAGGGAAGAG" " L-07","AGGCGGGAAC" " L-08","AGCAGGTGGA" " L-09","TGCGAGAGTC" " L-10","TGGGAGATGG" " L-11","ACGATGAGCC" " L-12","GGGCGGTACT" " L-13","ACCGCCTGCT" " L-14","GTGACAGGCT" " L-15","AAGAGAGGGG" " L-16","AGGTTGCAGG" " L-17","AGCCTGAGCC" " L-18","ACCACCCACC" " L-19","GAGTGGTGAC" " L-20","TGGTGGACCA" " M-01","GTTGGTGGCT" " M-02","ACAACGCCTC" " M-03","GGGGGATGAG" " M-04","GGCGGTTGTC" " M-05","GGGAACGTGT" " M-06","CTGGGCAACT" " M-07","CCGTGACTCA" " M-08","TCTGTTCCCC" " M-09","GTCTTGCGGA" " M-10","TCTGGCGCAC" " M-11","GTCCACTGTG" " M-12","GGGACGTTGG" " M-13","GGTGGTCAAG" " M-14","AGGGTCGTTC" " M-15","GACCTACCAC" " M-16","GTAACCAGCC" " M-17","TCAGTCCGGG" " M-18","CACCATCCGT" " M-19","CCTTCAGGCA" " M-20","AGGTCTTGGG" " N-01","CTCACGTTGG" " N-02","ACCAGGGGCA" " N-03","GGTACTCCCC" " N-04","GACCGACCCA" " N-05","ACTGAACGCC" " N-06","GAGACGCACA" " N-07","CAGCCCAGAG" " N-08","ACCTCAGCTC" " N-09","TGCCGGCTTG" " N-10","ACAACTGGGG" " N-11","TCGCCGCAAA" " N-12","CACAGACACC" " N-13","AGCGTCACTC" " N-14","TCGTGCGGGT" " N-15","CAGCGACTGT" " N-16","AAGCGACCTG" " N-17","CATTGGGGAG" " N-18","GGTGAGGTCA" " N-19","GTCCGTACTG" " N-20","GGTGCTCCGT" " O-01","GGCACGTAAG" " O-02","ACGTAGCGTC" " O-03","CTGTTGCTAC" " O-04","AAGTCCGCTC" " O-05","CCCAGTCACT" " O-06","CCACGGGAAG" " O-07","CAGCACTGAC" " O-08","CCTCCAGTGT" " O-09","TCCCACGCAA" " O-10","TCAGAGCGCC" " O-11","GACAGGAGGT" " O-12","CAGTGCTGTG" " O-13","GTCAGAGTCC" " O-14","AGCATGGCTC" " O-15","TGGCGTCCTT" " O-16","TCGGCGGTTC" " O-17","GGCTTATGCC" " O-18","CTCGCTATCC" " O-19","GGTGCACGTT" " O-20","ACACACGCTG" " P-01","GTAGCACTCC" " P-02","TCGGCACGCA" " P-03","CTGATACGCC" " P-04","GTGTCTCAGG" " P-05","CCCCGGTAAC" " P-06","GTGGGCTGAC" " P-07","GTCCATGCCA" " P-08","ACATCGCCCA" " P-09","GTGGTCCGCA" " P-10","TCCCGCCTAC" " P-11","AACGCGTCGG" " P-12","AAGGGCGAGT" " P-13","GGAGTGCCTC" " P-14","CCAGCCGAAC" " P-15","GGAAGCCAAC" " P-16","CCAAGCTGCC" " P-17","TGACCCGCCT" " P-18","GGCTTGGCCT" " P-19","GGGAAGGACA" " P-20","GACCCTAGTC" " Q-01","GGGACGATGG" " Q-02","TCTGTCGGTC" " Q-03","GGTCACCTCA" " Q-04","AGTGCGCTGA" " Q-05","CCGCGTCTTG" " Q-06","GAGCGCCTTG" " Q-07","CCCCGATGGT" " Q-08","CTCCAGCGGA" " Q-09","GGCTAACCGA" " Q-10","TGTGCCCGAA" " Q-11","TCTCCGCAAC" " Q-12","AGTAGGGCAC" " Q-13","GGAGTGGACA" " Q-14","GGACGCTTCA" " Q-15","GGGTAACGTG" " Q-16","AGTGCAGCCA" " Q-17","GAAGCCCTTG" " Q-18","AGGCTGGGTG" " Q-19","CCCCCTATCA" " Q-20","TCGCCCAGTC" " R-01","TGCGGGTCCT" " R-02","CACAGCTGCC" " R-03","ACACAGAGGG" " R-04","CCCGTAGCAC" " R-05","GACCTAGTGG" " R-06","GTCTACGGCA" " R-07","ACTGGCCTGA" " R-08","CCCGTTGCCT" " R-09","TGAGCACGAG" " R-10","CCATTCCCCA" " R-11","GTAGCCGTCT" " R-12","ACAGGTGCGT" " R-13","GGACGACAAG" " R-14","CAGGATTCCC" " R-15","GGACAACGAG" " R-16","CTCTGCGCGT" " R-17","CCGTACGTAG" " R-18","GGCTTTGCCA" " R-19","CCTCCTCATC" " R-20","ACGGCAAGGA" " S-01","CTACTGCGCT" " S-02","CCTCTGACTG" " S-03","CAGAGGTCCC" " S-04","CACCCCCTTG" " S-05","TTTGGGGCCT" " S-06","GATACCTCGG" " S-07","TCCGATGCTG" " S-08","TTCAGGGTGG" " S-09","TCCTGGTCCC" " S-10","ACCGTTCCAG" " S-11","AGTCGGGTGG" " S-12","CTGGGTGAGT" " S-13","GTCGTTCCTG" " S-14","AAAGGGGTCC" " S-15","CAGTTCACGG" " S-16","AGGGGGTTCC" " S-17","TGGGGACCAC" " S-18","CTGGCGAACT" " S-19","GAGTCAGCAG" " S-20","TCTGGACGGA" " T-01","GGGCCACTCA" " T-02","GGAGAGACTC" " T-03","TCCACTCCTG" " T-04","CACAGAGGGA" " T-05","GGGTTTGGCA" " T-06","CAAGGGCAGA" " T-07","GGCAGGCTGT" " T-08","AACGGCGACA" " T-09","CACCCCTGAG" " T-10","CCTTCGGAAG" " T-11","TTCCCCGCGA" " T-12","GGGTGTGTAG" " T-13","AGGACTGCCA" " T-14","AATGCCGCAG" " T-15","GGATGCCACT" " T-16","GGTGAACGCT" " T-17","CCAACGTCGT" " T-18","GATGCCAGAC" " T-19","GTCCGTATGG" " T-20","GACCAATGCC" " U-01","ACGGACGTCA" " U-02","CTGAGGTCTC" " U-03","CTATGCCGAC" " U-04","ACCTTCGGAC" " U-05","TTGGCGGCCT" " U-06","ACCTTTGCGG" " U-07","CCTGCTCATC" " U-08","GGCGAAGGTT" " U-09","CCACATCGGT" " U-10","ACCTCGGCAC" " U-11","AGACCCAGAG" " U-12","TCACCAGCCA" " U-13","GGCTGGTTCC" " U-14","TGGGTCCCTC" " U-15","ACGGGCCAGT" " U-16","CTGCGCTGGA" " U-17","ACCTGGGGAG" " U-18","GAGGTCCACA" " U-19","GTCAGTGCGG" " U-20","ACAGCCCCCA" " V-01","TGACGCATGG" " V-02","AGTCACTCCC" " V-03","CTCCCTGCAA" " V-04","CCCCTCACGA" " V-05","TCCGAGAGGG" " V-06","ACGCCCAGGT" " V-07","GAAGCCAGCC" " V-08","GGACGGCGTT" " V-09","TGTACCCGTC" " V-10","GGACCTGCTG" " V-11","CTCGACAGAG" " V-12","ACCCCCCACT" " V-13","ACCCCCTGAA" " V-14","AGATCCCGCC" " V-15","CAGTGCCGGT" " V-16","ACACCCCACA" " V-17","ACCGGCTTGT" " V-18","TGGTGGCGTT" " V-19","GGGTGTGCAG" " V-20","CAGCATGGTC" " W-01","CTCAGTGTCC" " W-02","ACCCCGCCAA" " W-03","GTCCGGAGTG" " W-04","CAGAAGCGGA" " W-05","GGCGGATAAG" " W-06","AGGCCCGATG" " W-07","CTGGACGTCA" " W-08","GACTGCCTCT" " W-09","GTGACCGAGT" " W-10","TCGCATCCCT" " W-11","CTGATGCGTG" " W-12","TGGGCAGAAG" " W-13","CACAGCGACA" " W-14","CTGCTGAGCA" " W-15","ACACCGGAAC" " W-16","CAGCCTACCA" " W-17","GTCCTGGGTT" " W-18","TTCAGGGCAC" " W-19","CAAAGCGCTC" " W-20","TGTGGCAGCA" " X-01","CTGGGCACGA" " X-02","TTCCGCCACC" " X-03","TGGCGCAGTG" " X-04","CCGCTACCGA" " X-05","CCTTTCCCTC" " X-06","ACGCCAGAGG" " X-07","GAGCGAGGCT" " X-08","CAGGGGTGGA" " X-09","GGTCTGGTTG" " X-10","CCCTAGACTG" " X-11","GGAGCCTCAG" " X-12","TCGCCAGCCA" " X-13","ACGGGAGCAA" " X-14","ACAGGTGCTG" " X-15","CAGACAAGCC" " X-16","CTCTGTTCGG" " X-17","GACACGGACC" " X-18","GACTAGGTGG" " X-19","TGGCAAGGCA" " X-20","CCCAGCTAGA" " Y-01","GTGGCATCTC" " Y-02","CATCGCCGCA" " Y-03","ACAGCCTGCT" " Y-04","GGCTGCAATG" " Y-05","GGCTGCGACA" " Y-06","AAGGCTCACC" " Y-07","AGAGCCGTCA" " Y-08","AGGCAGAGCA" " Y-09","AGCAGCGCAC" " Y-10","CAAACGTGGG" " Y-11","AGACGATGGG" " Y-12","AAGCCTGCGA" " Y-13","GGGTCTCGGT" " Y-14","GGTCGATCTG" " Y-15","AGTCGCCCTT" " Y-16","GGGCCAATGT" " Y-17","GACGTGGTGA" " Y-18","GTGGAGTCAG" " Y-19","TGAGGGTCCC" " Y-20","AGCCGTGGAA" " Z-01","TCTGTGCCAC" " Z-02","CCTACGGGGA" " Z-03","CAGCACCGCA" " Z-04","AGGCTGTGCT" " Z-05","TCCCATGCTG" " Z-06","GTGCCGTTCA" " Z-07","CCAGGAGGAC" " Z-08","GGGTGGGTAA" " Z-09","CACCCCAGTC" " Z-10","CCGACAAACC" " Z-11","CTCAGTCGCA" " Z-12","TCAACGGGAC" " Z-13","GACTAAGCCC" " Z-14","TCGGAGGTTC" " Z-15","CAGGGCTTTC" " Z-16","TCCCCATCAC" " Z-17","CCTTCCCACT" " Z-18","AGGGTCTGTG" " Z-19","GTGCGAGCAA" " Z-20","ACTTTGGCGG" "AA-01","AGACGGCTCC" "AA-02","GAGACCAGAC" "AA-03","TTAGCGCCCC" "AA-04","AGGACTGCTC" "AA-05","GGCTTTAGCC" "AA-06","GTGGGTGCCA" "AA-07","CTACGCTCAC" "AA-08","TCCGCAGTAG" "AA-09","AGATGGGCAG" "AA-10","TGGTCGGGTG" "AA-11","ACCCGACCTG" "AA-12","GGACCTCTTG" "AA-13","GAGCGTCGCT" "AA-14","AACGGGCCAA" "AA-15","ACGGAAGCCC" "AA-16","GGAACCCACA" "AA-17","GAGCCCGACT" "AA-18","TGGTCCAGCC" "AA-19","TGAGGCGTGT" "AA-20","TTGCCTTCGG" "AB-01","CCGTCGGTAG" "AB-02","GGAAACCCCT" "AB-03","TGGCGCACAC" "AB-04","GGCACGCGTT" "AB-05","CCCGAAGCGA" "AB-06","GTGGCTTGGA" "AB-07","GTAAACCGCC" "AB-08","GTTACGGACC" "AB-09","GGGCGACTAC" "AB-10","TTCCCTCCCA" "AB-11","GTGCGCAATG" "AB-12","CCTGTACCGA" "AB-13","CCTACCGTGG" "AB-14","AAGTGCGACC" "AB-15","CCTCCTTCTC" "AB-16","CCCGGATGGT" "AB-17","TCGCATCCAG" "AB-18","CTGGCGTGTC" "AB-19","ACACCGATGG" "AB-20","CTTCTCGGAC" "AC-01","TCCCAGCAGA" "AC-02","GTCGTCGTCT" "AC-03","CACTGGCCCA" "AC-04","ACGGGACCTG" "AC-05","GTTAGTGCGG" "AC-06","CCAGAACGGA" "AC-07","GTGGCCGATG" "AC-08","TTTGGGTGCC" "AC-09","AGAGCGTACC" "AC-10","AGCAGCGAGG" "AC-11","CCTGGGTCAG" "AC-12","GGCGAGTGTG" "AC-13","GACCCGATTG" "AC-14","GTCGGTTGTC" "AC-15","TGCCGTGAGA" "AC-16","CCTCCTACGG" "AC-17","CCTGGAGCTT" "AC-18","TTGGGGGAGA" "AC-19","AGTCCGCCTG" "AC-20","ACGGAAGTGG" "AD-01","CAAAGGGCGG" "AD-02","CTGAACCGCT" "AD-03","TCTCGCCTAC" "AD-04","GTAGGCCTCA" "AD-05","ACCGCATGGG" "AD-06","AAGTGCACGG" "AD-07","CCCTACTGGT" "AD-08","GGCAGGCAAG" "AD-09","TCGCTTCTCC" "AD-10","AAGAGGCCAG" "AD-11","CAATCGGGTC" "AD-12","AAGAGGGCGT" "AD-13","GGTTCCTCTG" "AD-14","GAACGAGGGT" "AD-15","TTTGCCCCGT" "AD-16","AACGGGCGTC" "AD-17","GGCAAACCCT" "AD-18","ACGAGAGGCA" "AD-19","CTTGGCACGA" "AD-20","TCTTCGGAGG" "AE-01","TGAGGGCCGT" "AE-02","TCGTTCACCC" "AE-03","CATAGAGCGG" "AE-04","CCAGCACTTC" "AE-05","CCTGTCAGTG" "AE-06","GGGGAAGACA" "AE-07","GTGTCAGTGG" "AE-08","CTGGCTCAGA" "AE-09","TGCCACGAGG" "AE-10","CTGAAGCGCA" "AE-11","AAGACCGGGA" "AE-12","CCGAGCAATC" "AE-13","TGTGGACTGG" "AE-14","GAGAGGCTCC" "AE-15","TGCCTGGACC" "AE-16","TCCGTGCTGA" "AE-17","GGCAGGTTCA" "AE-18","CTGGTGCTGA" "AE-19","GACAGTCCCT" "AE-20","TTGACCCCAG" "AF-01","CCTACACGGT" "AF-02","CAGCCGAGAA" "AF-03","GAAGGAGGCA" "AF-04","TTGCGGCTGA" "AF-05","CCCGATCAGA" "AF-06","CCGCAGTCTG" "AF-07","GGAAAGCGTC" "AF-08","CTCTGCCTGA" "AF-09","CCCCTCAGAA" "AF-10","GGTTGGAGAC" "AF-11","ACTGGGCCTC" "AF-12","GACGCAGCTT" "AF-13","CCGAGGTGAC" "AF-14","GGTGCGCACT" "AF-15","CACGAACCTC" "AF-16","TCCCGGTGAG" "AF-17","TGAACCGAGG" "AF-18","GTGTCCCTCT" "AF-19","GGACAAGCAG" "AF-20","CTCCGCACAG" "AG-01","CTACGGCTTC" "AG-02","CTGAGGTCCT" "AG-03","TGCGGGAGTG" "AG-04","GGAGCGTACT" "AG-05","CCCACTAGAC" "AG-06","GGTGGCCAAG" "AG-07","CACAGACCTG" "AG-08","AAGAGCCCTC" "AG-09","CCGAGGGGTT" "AG-10","ACTGCCCGAC" "AG-11","TTACGGTGGG" "AG-12","CTCCCAGGGT" "AG-13","GGCTTGGCGA" "AG-14","CTCTCGGCGA" "AG-15","CCCACACGCA" "AG-16","CCTGCGACAG" "AG-17","AGCGGAAGTG" "AG-18","GTGGGCATAC" "AG-19","AGCCTCGGTT" "AG-20","TGCGCTCCTC" "AH-01","TCCGCAACCA" "AH-02","CACTTCCGCT" "AH-03","GGTTACTGCC" "AH-04","CTCCCCAGAC" "AH-05","TTGCAGGCAG" "AH-06","GTAAGCCCCT" "AH-07","CCCTACGGAG" "AH-08","TTCCCGTGCC" "AH-09","AGAACCGAGG" "AH-10","GGGATGACCA" "AH-11","TCCGCTGAGA" "AH-12","TCCAACGGCT" "AH-13","TGAGTCCGCA" "AH-14","TGTGGCCGAA" "AH-15","CTACAGCGAG" "AH-16","CAAGGTGGGT" "AH-17","CAGTGGGGAG" "AH-18","GGGCTAGTCA" "AH-19","GGCAGTTCTC" "AH-20","GGAAGGTGAG" "AI-01","GGCATCGGCT" "AI-02","AGCCGTTCAG" "AI-03","GGGTCCAAAG" "AI-04","CTATCCTGCC" "AI-05","GTCGTAGCGG" "AI-06","TGCCGCACTT" "AI-07","ACGAGCATGG" "AI-08","AAGCCCCCCA" "AI-09","TCGCTGGTGT" "AI-10","TCGGGGCATC" "AI-11","ACGGCGATGA" "AI-12","GACGCGAACC" "AI-13","ACGCTGCGAC" "AI-14","TGGTGCACTC" "AI-15","GACACAGCCC" "AI-16","AAGGCACGAG" "AI-17","CCTCACGTCC" "AI-18","TCGCGGAACC" "AI-19","GGCAAAGCTG" "AI-20","CCTGTTCCCT" "AJ-01","ACGGGTCAGA" "AJ-02","TCGCACAGTC" "AJ-03","AGCACCTCGT" "AJ-04","GAATGCGACC" "AJ-05","CAGCGTTGCC" "AJ-06","GTCGGAGTGG" "AJ-07","CCCTCCCTAA" "AJ-08","GTGCTCCCTC" "AJ-09","ACGGCACGCA" "AJ-10","GTTACCGCGA" "AJ-11","GAACGCTGCC" "AJ-12","CAGTTCCCGT" "AJ-13","CAGCCGTTCC" "AJ-14","ACCGATGCTG" "AJ-15","GAATCCGGCA" "AJ-16","TCTGGACCGA" "AJ-17","ACCCCCTATG" "AJ-18","GGCTAGGTGG" "AJ-19","ACAGTGGCCT" "AJ-20","ACACGTGGTC" "AK-01","TCTGCTACGG" "AK-02","CCATCGGAGG" "AK-03","GGTCCTACCA" "AK-04","AGGGTCGGTC" "AK-05","GATGGCAGTC" "AK-06","TCACGTCCCT" "AK-07","CTTGGGGGAC" "AK-08","CCGAAGGGTG" "AK-09","AGGTCGGCGT" "AK-10","CAAGCGTCAC" "AK-11","CAGTGTGCTC" "AK-12","AGTGTAGCCC" "AK-13","TCCCACGAGT" "AK-14","CTGTCATGCC" "AK-15","ACCTGCCGTT" "AK-16","CTGCGTGCTC" "AK-17","CAGCGGTCAC" "AK-18","ACCCGGAAAC" "AK-19","TCGCAGCGAG" "AK-20","TGATGGCGTC" "AL-01","TGTGACGAGG" "AL-02","ACCCTGTGGG" "AL-03","CCCACCCTTG" "AL-04","ACAACGGTCC" "AL-05","GACTGCGCCA" "AL-06","AAGCGTCCTC" "AL-07","CCGTCCATCC" "AL-08","GTCGCCCTCA" "AL-09","CAGCGAGTAG" "AL-10","AAGGCCCCTG" "AL-11","GTCACGTCCT" "AL-12","CCCAGGCTAC" "AL-13","GAATGGCACC" "AL-14","TCGCTCCGTT" "AL-15","AGGGGACACC" "AL-16","CTTTCGAGGG" "AL-17","CCGCAAGTGT" "AL-18","GGAGTGGACT" "AL-19","TCTGCCAGTG" "AL-20","AGGAGTCGGA" "AM-01","TCACGTACGG" "AM-02","ACTTGACGGG" "AM-03","CTTCCCTGTG" "AM-04","GAGGGACCTC" "AM-05","GGGCTATGCC" "AM-06","CTCGGGATGT" "AM-07","AACCGCGGCA" "AM-08","ACCACGAGTG" "AM-09","TGCCGGTTCA" "AM-10","CAGACCGACC" "AM-11","AGATGCGCGG" "AM-12","TCTCACCGTC" "AM-13","CACGGCACAA" "AM-14","TGGTTGCGGA" "AM-15","GATGCGATGG" "AM-16","TGGCGGTTTG" "AM-17","CCTAACGTCC" "AM-18","ACGGGACTCT" "AM-19","CCAGGTCTTC" "AM-20","ACCAACCAGG" "AN-01","ACTCCACGTC" "AN-02","CACCGCAGTT" "AN-03","AGCCAGGCTG" "AN-04","GGCGTAAGTC" "AN-05","GGGTGCAGTT" "AN-06","GGGAACCCGT" "AN-07","TCGCTGCGGA" "AN-08","AAGGCTGCTG" "AN-09","GGGGGAGATG" "AN-10","CTGTGTGCTC" "AN-11","GTCCATGCAG" "AN-12","AACGGCGGTC" "AN-13","CTTCCAGGAC" "AN-14","AGCCGGGTAA" "AN-15","TGATGCCGCT" "AN-16","GTGTCGAGTC" "AN-17","TCAGCACAGG" "AN-18","TGTCCTGCGT" "AN-19","ACCACGCCTT" "AN-20","GAGTCCTCAC" "AO-01","AAGACGACGG" "AO-02","AATCCGCTGG" "AO-03","AGTCGGCCCA" "AO-04","AACAGGGCAG" "AO-05","TGGAAGCACC" "AO-06","AGGCAGCCTG" "AO-07","GATGCGACGG" "AO-08","ACTGGCTCTC" "AO-09","CCAGATGGGG" "AO-10","GACATCGTCC" "AO-11","GGGGGCTTGA" "AO-12","TCCCGGTCTC" "AO-13","CCCACAGGTG" "AO-14","CTACTGGGGT" "AO-15","GAAGGCTCCC" "AO-16","CACAACGGGA" "AO-17","CCCATGTGTG" "AO-18","GGGAGCGCTT" "AO-19","GTTCTCGGAC" "AO-20","GGCTTGCCTG" "AP-01","AACTGGCCCC" "AP-02","TGGTCATCCC" "AP-03","GTAAGGCGCA" "AP-04","CTCTTGGGCT" "AP-05","GACTTCAGGG" "AP-06","GTCACGTCTC" "AP-07","ACCACCCGCT" "AP-08","ACCCCCACAC" "AP-09","GTGGTCCAGA" "AP-10","TGGGTGATCC" "AP-11","CTGGCTTCTG" "AP-12","GTCTTACCCC" "AP-13","TGAAGCCCCT" "AP-14","TGCCATGCTG" "AP-15","GGGTTGGAAG" "AP-16","GGGCAGATAC" "AP-17","ACGGCACTCC" "AP-18","GTCGTCGACA" "AP-19","GTGTCTGCCT" "AP-20","CCCGGATACA" "AQ-01","GGCAGGTGGA" "AQ-02","ACCCTCGGAC" "AQ-03","GAGGTGTCTG" "AQ-04","GACGGCTATC" "AQ-05","ACGGAGCTGA" "AQ-06","ACGGATCCCC" "AQ-07","GGAGTAACGG" "AQ-08","TCGGTAGACC" "AQ-09","AGTCCCCCTC" "AQ-10","CATACCCTCC" "AQ-11","GACGCCTCCA" "AQ-12","CAGCTCCTGT" "AQ-13","GAGTCGGCTG" "AQ-14","CCCGTGTAGG" "AQ-15","TGCGATGCGA" "AQ-16","CCCGGAAGAG" "AQ-17","TTCGCCTGTC" "AQ-18","GGGAGCGAGT" "AQ-19","AGTAGGGCCT" "AQ-20","GTGAACGCTC" "AR-01","CCATTCCGAG" "AR-02","CACCTGCTGA" "AR-03","GTGAGGCGCA" "AR-04","CCAGGAGAAG" "AR-05","CATACCTGCC" "AR-06","TGGGGCTCAA" "AR-07","TCCTTCGGTG" "AR-08","GTGAATGCGG" "AR-09","GGGGTGTTCT" "AR-10","TGGGGCTGTC" "AR-11","GGGAAGACGG" "AR-12","GGATCGTCGG" "AR-13","GGGTCGGCTT" "AR-14","CTCACAGCAC" "AR-15","ACACTCTGCC" "AR-16","CCTTGCGCCT" "AR-17","CCACCACGAC" "AR-18","CTACCGGCAC" "AR-19","CTGATCGCGG" "AR-20","TGCGCCATCC" "AS-01","CACACCGTGT" "AS-02","GTCCTCGTGT" "AS-03","ACGGTTCCAC" "AS-04","GTCTTGGGCA" "AS-05","GTCACCTGCT" "AS-06","GGCGCGTTAG" "AS-07","GACGAGCAGG" "AS-08","GGCTGCCAGT" "AS-09","TGGAGTCCCC" "AS-10","CCCGTCTACC" "AS-11","ACCGTGCCGT" "AS-12","TGACCAGGCA" "AS-13","CACGGACCGA" "AS-14","TCGCAGCGTT" "AS-15","CTGCAATGGG" "AS-16","AACCCTTCCC" "AS-17","AGTTCCGCGA" "AS-18","GTTGCGCAGT" "AS-19","TGACAGCCCC" "AS-20","TCTGCCTGGA" "AT-01","CAGTGGTTCC" "AT-02","CAGGTCTAGG" "AT-03","GACTGGGAGG" "AT-04","TTGCCTCGCC" "AT-05","ACACCTGCCA" "AT-06","CCGTCCCTGA" "AT-07","ACTGCGACCA" "AT-08","TCCTCGTGGG" "AT-09","CCGTTAGCGT" "AT-10","ACCTCCGGTC" "AT-11","CCAGATCTCC" "AT-12","CTGCCTAGCC" "AT-13","CTGGTGGAAG" "AT-14","GTGCCGCACT" "AT-15","TGACGCACGG" "AT-16","CTCTCCGTAG" "AT-17","AGCGACTGCT" "AT-18","CCAGCTGTGA" "AT-19","ACCAAGGCAC" "AT-20","ACATCAGCCC" "AU-01","GGGATGGAAC" "AU-02","CCAACCCGCA" "AU-03","ACGAAACGGG" "AU-04","GGCTTCTGTC" "AU-05","GAGCTACCGT" "AU-06","TCTCTAGGGG" "AU-07","AGACCCTTGG" "AU-08","CACCGATCCA" "AU-09","ACGGCCAATC" "AU-10","GGCGTATGGT" "AU-11","CTTCTCGGTC" "AU-12","CCACTCGTGT" "AU-13","CCAAGCACAC" "AU-14","CACCTCGACC" "AU-15","TGCTGACGAC" "AU-16","TCTTAGGCGG" "AU-17","TTGGCATCCC" "AU-18","CACCACTAGG" "AU-19","AGCCTGGGGA" "AU-20","GTCGAAACCC" "AV-01","TGAGGGGGAA" "AV-02","TCACCGTGTC" "AV-03","TGTAGCCGTG" "AV-04","TCTGCCATCC" "AV-05","GTGAGCGTGG" "AV-06","CCCGAGATCC" "AV-07","CTACCAGGGA" "AV-08","TGAGAAGCGG" "AV-09","GAGGTCCTAC" "AV-10","ACCCCTGGCA" "AV-11","GACCCCGACA" "AV-12","AGCCGTCGAA" "AV-13","CTGACTTCCC" "AV-14","CTCCGGATCA" "AV-15","GGCAGCAGGT" "AV-16","GACAAGGACC" "AV-17","CTCGAACCCC" "AV-18","TTGCTCACGG" "AV-19","CTCGATCACC" "AV-20","TCATGCGCAC" "AW-01","ACCTAGGGGA" "AW-02","TCGCAGGTTC" "AW-03","CCATGCGGAG" "AW-04","AGGAGCGACA" "AW-05","CTGCTTCGAG" "AW-06","TTTGGGCCCC" "AW-07","AGCCCCCAAG" "AW-08","CTGTCTGTGG" "AW-09","ACTGGGTCGG" "AW-10","GGTGTTTGCC" "AW-11","CTGCCACGAG" "AW-12","GAGCAAGGCA" "AW-13","CTACGATGCC" "AW-14","GGTTCTGCTC" "AW-15","CCAGTCCCAA" "AW-16","TTACCCCGCT" "AW-17","TGCTGCTGCC" "AW-18","GGCGCAACTG" "AW-19","GGACACAGAG" "AW-20","TGTCCTAGCC" "AX-01","GTGTGCCGTT" "AX-02","GGGAGGCAAA" "AX-03","CCAAGAGGCT" "AX-04","TCCCCAGGAG" "AX-05","AGTGCACACC" "AX-06","AGGCATCGTG" "AX-07","ACGCGACAGA" "AX-08","AGTATGGCGG" "AX-09","GGAAGTCCTG" "AX-10","CCAGGCTGAC" "AX-11","TGATTGCGGG" "AX-12","GGTCGGGTCA" "AX-13","GAGCACTGCT" "AX-14","CACGGGCTTG" "AX-15","CAGCAATCCC" "AX-16","GTCTGTGCGG" "AX-17","TGGGCTCTGG" "AX-18","GTGTGCAGTG" "AX-19","CCCTGTCGCA" "AX-20","ACACTCGGCA" From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!UNIXG.UBC.CA!hobbs From: hobbs@UNIXG.UBC.CA Newsgroups: bionet.molbio.rapd Subject: UBC Primer Sequences Message-ID: <9309092200.AA10214@unixg.ubc.ca> Date: 9 Sep 93 23:01:42 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 723 Doug Rhoads has just posted the list of the presently extant 700 UBC RAPD primer sequences, and for this I am indebted to him. In fact, since Toby Bradshaw posted the Operon sequences earlier today (thanks, Toby) I spent the early part of this afternoon cudgelling the full list of UBC sequences into a format I could post, so here it is. This should, of course, duplicate the information which Doug has made available; I'm sure his students copied them all correctly, but, rather than check through 700 sequences, I thought I'd simply post my file. The sequence data have of course been freely available to all who asked for them for some time. UBC Set #8 is presently in preparation, and I will give further details and the sequences when it is ready. 1. CCT GGG CTT C 2. CCT GGG CTT G 3. CCT GGG CTT A 4. CCT GGG CTG G 5. CCT GGG TTC C 6. CCT GGG CCT A 7. CCT GGG GGT T 8. CCT GGC GGT A 9. CCT GCG CTT A 10. GGG GGG ATT A 11. CCC CCC TTT A 12. CCT GGG TCC A 13. CCT GGG TGG A 14. CCT GGG TTT C 15. CCT GGG TTT G 16. GGT GGC GGG A 17. CCT GGG CCT C 18. GGG CCG TTT A 19. GCC CGG TTT A 20. TCC GGG TTT G 21. ACC GGG TTT C 22. CCC TTG GGG G 23. CCC GCC TTC C 24. ACA GGG GTG A 25. ACA GGG CTC A 26. TTT GGG CCC A 27. TTT GGG GGG A 28. CCG GCC TTA A 29. CCG GCC TTA C 30. CCG GCC TTA G 31. CCG GCC TTC C 32. GGG GCC TTA A 33. CCG GCT GGA A 34. CCG GCC CCA A 35. CCG GGG TTA A 36. CCC CCC TTA G 37. CCG GGG TTT T 38. CCG GGG AAA A 39. TTA ACC GGG C 40. TTA CCT GGG C 41. TTA ACC GGG G 42. TTA ACC CGG C 43. AAA ACC GGG C 44. TTA CCC CGG C 45. TTA ACC CCG G 46. TTA AGG GGG C 47. TTC CCC AAG C 48. TTA ACG GGG A 49. TTC CCC GAG C 50. TTC CCC GCG C 51. CTA CCC GTG C 52. TTC CCG GAG C 53. CTC CCT GAG C 54. GTC CCA GAG C 55. TCC CTC GTG C 56. TGC CCC GAG C 57. TTC CCC GAG G 58. TTC CCG GAG C 59. TTC CGG GTG C 60. TTG GCC GAG C 61. TTC CCC GAC C 62. TTC CCC GTC G 63. TTC CCC GCC C 64. GAG GGC GGG A 65. AGG GGC GGG A 66. GAG GGC GTG A 67. GAG GGC GAG C 68. GAG CTC GCG A 69. GAG GGC AAG A 70. GGG CAC GCG A 71. GAG GGC GAG G 72. GAG CAC GGG A 73. GGG CAC GCG A 74. GAG CAC CTG A 75. GAG GTC CAG A 76. GAG CAC CAG T 77. GAG CAC CAG G 78. GAG CAC TAG C 79. GAG CTC GTG T 80. GTG CTC TAG A 81. GAG CAC GGG G 82. GGG CCC GAG G 83. GGG CTC GTG G 84. GGG CGC GAG T 85. GTG CTC GTG C 86. GGG GGG AAG G 87. GGG GGG AAG C 88. CGG GGG ATG G 89. GGG GGC TTG G 90. GGG GGT TAG G 91. GGG TGG TTG C 92. CCT GGG CTT T 93. GGG GGG AAA G 94. GGG GGG AAC C 95. GGG GGG TTG G 96. GGC GGC ATG G 97. ATC TGC GAG C 98. ATC CTG CCA G 99. ATC CCC TGG G 100 ATC GGG TCC G 101. GCG GCT GGA G 102. GGT GGG GAC T 103. GTG ACG CCG C 104. GGG CAA TGA T 105. CTC GGG TGG G 106. CGT CTG CCC G 107. CTG TCC CTT T 108. GTA TTG CCC T 109. TGT ACG TGA C 110. TAG CCC GCT T 111. AGT AGA CGG G 112. GCT TGT GAA C 113. ATC CCA AGA G 114. TGA CCG AGA C 115. TTC CGC GGG C 116. TAC GAT GAC G 117. TTA GCG GTC T 118. CCC GTT TTG T 119. ATT GGG CGA T 120. GAA TTT CCC C 121. ATA CAG GGA G 122. GTA GAC GAG C 123. GTC TTT CAG G 124. ACT CGA AGT C 125. GCG GTT GAG G 126. CTT TCG TGC T 127. ATC TGG CAG C 128. GCA TAT TCC G 129. GCG GTA TAG T 130. GGT TAT CCT C 131. GAA ACA GCG T 132. AGG GAT CTC C 133. GGA AAC CTC T 134. AAC ACA CGA G 135. AAG CTG CGA G 136. TAC GTC TTG C 137. GGT CTC TCC C 138. GCT TCC CCT T 139. CCC AAT CTT C 140. GTC GCA TTT C 141. ATC CTG TTC G 142. ATC TGT TCG G 143. TCG CAG AAC G 144. AGA GGG TTC T 145. TGT CGG TTG C 146. ATG TGT TGC G 147. GTG CGT CCT C 148. TGT CCA CCA G 149. AGC AGC GTG G 150. GAA GGC TCT G 151. GCT GTA GTG T 152. CGC ACC GCA C 153. GAG TCA CGA G 154. TCC ATG CCG T 155. CTG GCG GCT G 156. GCC TGG TTG C 157. CGT GGG CAG G 158. TAG CCG TGG C 159. GAG CCC GTA G 160. CGA TTC AGA G 161. CGT TAT CTC G 162. AAC TTA CCG C 163. CCC CCC AGA T 164. CCA AGA TGC T 165. GAA GGC ACT G 166. ACT GCT ACA G 167. CCA ATT CAC G 168. CTA GAT GTG C 169. ACG ACG TAG G 170. ATC TCT CCT G 171. TGA CCC CTC C 172. ACC GTC GTA G 173. CAG GCG GCG T 174. AAC GGG CAG C 175. TGG TGC TGA T 176. CAA GGG AGG T 177. TCA GGC AGT C 178. CCG TCA TTG G 179. TCA CTG TAC G 180. GGG CCA CGC T 181. ATG ACG ACG G 182. GTT CTC GTG T 183. CGT GAT TGC T 184. CAA ACG GCA C 185. GTG TCT TCA C 186. GTG CGT CGC T 187. AAC GGG GGA G 188. GCT GGA CAT C 189. TGC TAG CCT C 190. AGA ATC CGC C 191. CGA TGG CTT T 192. GCA AGT CAC T 193. TGC TGG CTT T 194. AGG ACG TGC C 195. GAT CTC AGC G 196. CTC CTC CCC C 197. TCC CCG TTC C 198. GCA GGA CTG C 199. GCT CCC CCA C 200. TCG GGA TAT G 201. CTG GGG ATT T 202. GAG CAC TTA C 203. CAC GGC GAG T 204. TTC GGG CCG T 205. CGG TTT GGA A 206. GAG GAC GTC C 207. CAT ATC AGG G 208. ACG GCC GAC C 209. TGC ACT GGA G 210. GCA CCG AGA G 211. GAA GCG CGA T 212. GCT GCG TGA C 213. CAG CGA ACT A 214. CAT GTG CTT G 215. TCA CAC GTG C 216. CAT AGA CTC C 217. ACA GGT AGA C 218. CTC AGC CCA G 219. GTG ACC TCA G 220. GTC GAT GTC G 221. CCC GTC AAT A 222. AAG CCT CCC C 223. GAT CCA TTG C 224. TCT CCG GTA T 225. CGA CTC ACA G 226. GGG CCT CTA T 227. CTA GAG GTC C 228. GCT GGG CCG A 229. CCA CCC AGA G 230. CGT CGC CCA T 231. AGG GAG TTC C 232. CGG TGA CAT C 233. CTA TGC GCG C 234. TCC ACG GAC G 235. CTG AGG CAA A 236. ATC GTA CGT G 237. CGA CCA GAG C 238. CTG TCC AGC A 239. CTG AAG CGG A 240. ATG TTC CAG G 241. GCC CGA CGC G 242. CAC TCT TTG C 243. GGG TGA ACC G 244. CAG CCA ACC G 245. CGC GTG CCA G 246. TAT GGT CCG G 247. TAC CGA CGG A 248. GAG TAA GCG G 249. GCA TCT ACC G 250. CGA CAG TCC C 251. CTT GAC GGG G 252. CTG GTG ATG T 253. CCG TGC AGT A 254. CGC CCC CAT T 255. TTC CTC CGG A 256. TGC AGT CGA A 257. CGT CAC CGT T 258. CAG GAT ACC A 259. GGT ACG TAC T 260. TCT CAG CTA C 261. CTG GCG TGA C 262. CGC CCC CAG T 263. TTA GAG ACG G 264. TCC ACC GAG C 265. CAG CTG TTC A 266. CCA CTC ACC G 267. CCA TCT TGT G 268. AGG CCG CTT A 269. CCA GTT CGC C 270. TGC GCG CGG G 271. GCC ATC AAG A 272. AGC GGG CCA A 273. AAT GTC GCC A 274. GTT CCC GAG T 275. CCG GGC AAG C 276. AGG ATC AAG C 277. AGG AAG GTG C 278. GGT TCC AGC T 279. AGA CAT TAG A 280. CTG GGA GTG G 281. GAG AGT GGA A 282. GGG AAA GCA G 283. CGG CCA CCG T 284. CAG GCG CAC A 285. GGG CGC CTA G 286. CGG AGC CGG C 287. CGA ACG GCG G 288. CCT CCT TGA C 289. ATC AAG CTG C 290. CCG CGA GCA C 291. AGC TGA AGA G 292. AAA CAG CCC G 293. TCG TGT TGC T 294. TGA TTG GCC A 295. CGC GTT CCT G 296. CCG CTG GGA G 297. GCG CAT TAG A 298. CCG TAC GGA C 299. TGT CAG CGG T 300. GGC TAG GGC G 301. CGG TGG CGA A 302. CGG CCC ACG T 303. GCG GGA GAC C 304. AGT CCT CGC C 305. GCT GGT ACC C 306. GTC CTC GTA G 307. CGC ATT TGC A 308. AGC GGC TAG G 309. ACA TCC TGC G 310. GAG CCA GAA G 311. GGT AAC CGT A 312. ACG GCG TCA C 313. ACG GCA GTG G 314. ACT TCC TCC A 315. GGT CTC CTA G 316. CCT CAC CTG T 317. CTA GGG GCT G 318. CGG AGA GCG A 319. GTG GCC GCG C 320. CCG GCA TAG A 321. ATC TAG GGA C 322. GCC GCT ACT A 323. GAC ATC TCG C 324. ACA GGG AAC G 325. TCT AAG CTC G 326. CGG ATC TCT A 327. ATA CGG CGT C 328. ATG GCC TTA C 329. GCG AAC CTC C 330. GGT GGT TTC C 331. GCC TAG TCA C 332. AAC GCG TAG A 333. GAA TGC GAC G 334. ATG GCA AAG C 335. TGG ACC ACC C 336. GCC ACG GAG A 337. TCC CGA ACC G 338. CTG TGG CGG T 339. CTC ACT TGG G 340. GAG AGG CAC C 341. CTG GGG CCG T 342. GAG ATC CCT C 343. TGT TAG GCT C 344. TGT TAG GCA C 345. GCG TGA CCC G 346. TAG GCG AAC G 347. TTG CTT GGC G 348. CAC GGC TGC G 349. GGA GCC CCC T 350. TGA CGC GCT C 351. CTC CCG GTG G 352. CAC AAC GGG T 353. TGG GCT CGC T 354. CTA GAG GCC G 355. GTA TGG GGC T 356. GCG GCC CTC T 357. AGG CCA AAT G 358. GGT CAG GCC C 359. AGG CAG ACC T 360. CTC TCC AGG C 361. GCG AGG TGC T 362. CCG CCT TAC A 363. ATG ACG TTG A 364. GGC TCT CGC G 365. TAG ACA GAG G 366. CCT GAT TGC C 367. ACC TTT GGC T 368. ACT TGT GCG G 369. GCG CAT AGC A 370. TCA GCC AGC G 371. TCT CGA TTG C 372. CCC ACT GAC G 373. CTG AGG AGT G 374. GGT CAA CCC T 375. CCG GAC ACG A 376. CAG GAC ATC G 377. GAC GGA AGA G 378. GAC AAC AGG A 379. GGG CTA GGG T 380. AGG AGT GAG A 381. ATG AGT CCT G 382. ATA CAC CAG C 383. GAG GCG CTG C 384. TGC GCC GCT A 385. ACC GGG AAC G 386. TGT AAG CTC G 387. CGC TGT CGC C 388. CGG TCG CGT C 389. CGC CCG CAG T 390. TCA CTC AGA G 391. GCG AAC CTC G 392. CCT GGT GGT T 393. TTC CAT GCC T 394. TCA CGC AGT T 395. TCA CTT GAG G 396. GAA TGC GAG G 397. GGG CTG TGC C 398. CAG TGC TCT T 399. TTG CTG GGC G 400. GCC CTG ATA T 401. TAG GAC AGT C 402. CCC GCC GTT G 403. GGA AGG CTG T 404. TCT CTA CGA C 405. CTC TCG TGC G 406. GCC ACC TCC T 407. TGG TCC TGG C 408. CCG TCT CTT T 409. TAG GCG GCG G 410. CGT CAC AGA G 411. GAG GCC CGT T 412. TGC GCC GGT G 413. GAG GCG GCG A 414. AAG GCA CCA G 415. GTT CCA GCA G 416. GTG TTT CCG G 417. GAC AGG CCA A 418. GAG GAA GCT T 419. TAC GTG CCC G 420. GCA GGG TTC G 421. ACG GCC CAC C 422. CAC CTG CGG G 423. GGG TCT CGA A 424. ACG GAG GTT C 425. CGT CGG GCC T 426. TCT CCC GGT G 427. GTA ATC GAC G 428. GGC TGC GGT A 429. AAA CCT GGA C 430. AGT CGG CAC C 431. CTG CGG GTC A 432. AGC GTC GAC T 433. TCA CGT GCC T 434. TCG CTA GTC C 435. CTA GTA GGG G 436. GAG GGG GCC A 437. AGT CCG CTG C 438. AGA CGG CCG G 439. GCC CCT TGA C 440. CTG TCG AAC C 441. CTG CGT TCT T 442. CTA CTC GGT T 443. TGA TTG CTC G 444. GCA GCC CCA T 445. TAG CAG CTT G 446. GCC AGC GTT C 447. CAG GCT CTA G 448. GTT GTG CCT G 449. GAG GTT CAA C 450. CGG AGA GCC C 451. CTA ATC TCG C 452. CTA ATC ACG G 453. AGT ACA AGG G 454. GCT TAC GGC A 455. AGC AAG CCG G 456. GCG GAG GTC C 457. CGA CGC CCT G 458. CTC ACA TGC C 459. GCG TCG AGG G 460. ACT GAC CGG C 461. CCC GTA TGT C 462. CAT AGC GGC A 463. AGG CGG AAG C 464. CAC AAG CCT G 465. GGT CAG GGC T 466. TTC TTA GCG G 467. AGC ACG GGC A 468. ACG GAA GCG C 469. CTC CAG CAA A 470. AGG AGC TGG G 471. CCG ACC GGA A 472. AGG CGT GCA A 473. ATC CCC AAG A 474. AGG CGG GAA C 475. CCA GCG TAT T 476. TTG AGG CCC T 477. TGT TGT GCC C 478. CGA GCT GGT C 479. CTC ATA CGC G 480. GGA GGG GGG A 481. GTA ATT GCG C 482. CTA TAG GCC G 483. GCA CTA AGA C 484. CTG GCA AGG A 485. AGA ATA GGG C 486. CCA GCA TCA G 487. GTG GCT AGG T 488. TTC GCT TCT C 489. CGC ACG CAC A 490. AGT CGA CCT T 491. TCC TGT CAA G 492. GTG ACT GCT C 493. CCG AAT CAC T 494. TGA TGC TGT C 495. CTT TCC TTC C 496. CCT TTC AAG G 497. GCA TAG TGC G 498. GAC AGT CCT G 499. GGC CGA TGA T 500. TTG CGT CAT G 501. CGG ATA TAC C 502. GCA TGG TAG C 503. ATC GTC CAA C 504. ACC GTG CGT C 505. CCC TTT ACA C 506. CCT TTC CCG A 507. AGA CGT ACT C 508. CGG GGC GGA A 509. ACA GAG ACT G 510. CGC ATC TCT T 511. GAA TGG TGA G 512. GGG TGG ACA T 513. TAT ACG ACC C 514. CGG TTA GAC G 515. GGG GGC CTC A 516. AGC GCC GAC G 517. GGT CGC AGC T 518. TGC TGG TCC A 519. ACC GGA CAC T 520. TGC GCA GCC C 521. CCG CCC CAC T 522. TCG TCT AGC A 523. ACA GGC AGA C 524. CGG TTA CTA G 525. GCT GGT TGG A 526. AAC GGG CAC C 527. CTT CAA CGT G 528. GGA TCT ATG C 529. CAC TCC TAC A 530. AAT AAC CGC C 531. GCT CAC TGT T 532. TTG AGA CAG G 533. GCA TCT ACG C 534. CAC CCC CTG C 535. CCA CCA ACA G 536. GCC CCT CGT C 537. CGA AAG GAC T 538. TGA CCT CTC C 539. CTT ACG TCA C 540. CGG ACC GCG T 541. GCC CCT TTA C 542. CCC ATG GCC C 543. CGC TTC GGG T 544. TAG AGA CTC C 545. ACG TTG AGA C 546. CCC GCA GAG T 547. TAT GAC CTG G 548. GTA CAT GGG C 549. CCG GCT TAT G 550. GTC GCC TGA G 551. GGA AGT CCA C 552. CTA AAT GGC G 553. TCC GAG ATC G 554. TCA TCC AGG G 555. GTG AAC AGC A 556. ATG GAT GAC G 557. GTG TAG AGC C 558. CGA TAT CCG G 559. GAG AAC TGG C 560. CAC TGC TGT C 561. CAT AAC GAC C 562. CAA AGT AGC C 563. CGC CGC TCC T 564. CGG CGT TAC G 565. GGT CGA TTT C 566. CCA CAT GCG A 567. AGA CAC CTG A 568. ACC TGT TCT C 569. CGA ATT GCT G 570. GGC CGC TAA T 571. GCG CGG CAC T 572. TTC GAC CAT C 573. CCC TAA TCA G 574. GCC AGA CAA G 575. GGA GAT GTA C 576. CAC CTA ATG G 577. GTC TGA TGT G 578. GGT GTC CAC T 579. TGG AAT CGT G 580. GCG ATA GTC C 581. CCC GTT AAG G 582. GGT ATA GAC G 583. GTA TTT GCG C 584. GCG GGC AGG A 585. CCC GCG AGT C 586. CCG GTT CCA G 587. GCT ACT AAC C 588. CAG AGG TTG G 589. GAC GGA GGT C 590. CCG GCA TGT T 591. TCC CTC GTG G 592. GGG CGA GTG C 593. CGA GCT TTG A 594. AGG AGC TGG C 595. GTC ACC GCG C 596. CCC CTC GAA T 597. TGG TTC CCG A 598. ACG GGC GCT C 599. CAA GAA CCG C 600. GAA GAA CCG C 601. CCG CCC ACT G 602. GCG AAG ACT A 603. ACC CAC CGC G 604. GGC CCA TTG C 605. CCG ATC ATT C 606. CGG TCG GCC A 607. AGT GTC GTC G 608. GAG CCC GAA A 609. ACA GCA CCA T 610. TTT GCC GCC C 611. CCA TCG TAC C 612. CCG TGA GTA T 613. TGC ACC CAC G 614. GTA GTC TCG C 615. CGT CGA GCG G 616. CGG AAG AAA C 617. CGG ACT ATG T 618. CGG ACT ATG T 619. TTC CCT AGC G 620. TTG CGC CCG G 621. GTC TGC GCT A 622. ACA GGT GGT T 623. TGC GGG ACT G 624. GTG ATA AGC C 625. CCG CTG GAG C 626. CCA AGC CCG G 627. GGA TTC ACA G 628. GTC TGG TTA G 629. GCA AGT ATG C 630. CAC TCT CTG G 631. GGC TTA ACC G 632. GAG TTT ACC C 633. CGT TGT ATC C 634. CCG TAC ACG C 635. CTC AGC TCA G 636. GGG ATA TCG C 637. CCC TAA AGC G 638. GCG GTG ACT A 639. ATC GAG CAC C 640. CGT GGG GCC T 641. TGG AAC CAT G 642. GTG GTC TCG A 643. ATA AGC GGT G 644. TCG TAT TGG G 645. TAC AGC GTT G 646. GTC CAC TTC C 647. CCT GTG GGG G 648. GCA CGC GAG A 649. AAT GCT GGA C 650. AGT ATG CAG C 651. TCA TTT CGC C 652. CCC AAC ACA C 653. CAT GCA AGA C 654. CCC TGG TCT G 655. GCA TTT CCC G 656. CGT AAC CTT G 657. GTC CTT TAG C 658. CCT ATG TAC C 659. CGG TTT CGT A 660. AGA CGC CGA C 661. CCT GCT TAC G 662. GGC TAC GTC T 663. CGT ATA GCC G 664. GCC TGA AAA C 665. GAC GCT TTT C 666. CTT AAC ACG C 667. CGC AGA AAT C 668. CCC GAT TGA G 669. GTT ACA CCA C 670. CCC TTG AGA C 671. CAT TAA GGC G 672. TAC CGT GGC G 673. TTC ATA CGC G 674. ATC GAT CCG G 675. ACC GGT GGA G 676. GCT AAC GTC C 677. TCT CAG GAC A 678. AGC GGA GCT G 679. GAT GGG GTG G 680. AAT GAG AGC C 681. CCC CCG GAC T 682. CTG CGA CGG T 683. TAT TAC CGC C 684. CCA CAC GTA G 685. GAT CGC AGG C 686. CGT GAC AGG A 687. ATA CAA GGG G 688. GCA GGA GCG T 689. TGT CCG GAA G 690. TAA TCC GGT C 691. AAA CCA GGC G 692. ACA TTG GGG G 693. GAC GAG ACG G 694. GGT TTG GAG G 695. GCT AAT CAG C 696. CGG ACA TGG C 697. CGC AGG TCA C 698. CTA GAC GTT G 699. GTT ACT GCC C 700. GGA CTA AGG T Dr. John Hobbs Nucleic Acid - Protein Service (NAPS) Unit Biotechnology Laboratory Room 237, Wesbrook Building 6174 University Boulevard University of British Columbia Vancouver, V6T 1Z3 Canada. FAX (604)822-5437; Tel. (604)822-6373 From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!LIMARMG%BRUFMG From: LIMARMG%BRUFMG@UICVM.UIC.EDU (Lima RMG) Newsgroups: bionet.molbio.rapd Subject: AFLP Message-ID: <9309092201.AA24527@net.bio.net> Date: 9 Sep 93 22:01:29 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Dear Sirs, I'm very interested in this new technique and who have some reference about it? Roberto Lima Departamento de Zootecnia, UFMG BITNET LIMARMG@BRUFMG From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!uunet!spool.mu.edu!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Re: List of UBC primers & List of Operon primers Message-ID: <26o6pg$be2@overload.lbl.gov> Date: 9 Sep 93 21:21:52 GMT References: <455BCAF2CA9@uamercury.uark.edu> Distribution: bionet Organization: Dendrome, A Genome Database for Forest Trees Lines: 31 NNTP-Posting-Host: s27w007.pswfs.gov In article <455BCAF2CA9@uamercury.uark.edu> DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") writes: >Since others have posted the list of Operon primers I would like to >contribute the list of UBC primers. I can't guarantee they all are >correct as supplied by John Hobbs but the students in my lab tried to get >them entered correctly. > ... I have a list of UBC primers supplied by John Hobbs and I have added the list of Operon primers posted by Toby Bradshaw to the Dendrome project Gopher server. Here's a gopher link: # Type=1 Name=Reagents Path=1/.Forest_Tree_Genomes/Reagents Host=s27w007.pswfs.gov Port=70 or just point your gopher client at s27w007.pswfs.gov [192.131.1.21]. --bks Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!torn!csd.unb.ca!news.ucs.mun.ca!kean.ucs.mun.ca!scarr From: scarr@kean.ucs.mun.ca Newsgroups: bionet.molbio.rapd Subject: delete subscription Message-ID: <1993Sep9.191613.1@kean.ucs.mun.ca> Date: 9 Sep 93 22:46:13 GMT Sender: usenet@news.ucs.mun.ca (NNTP server account) Organization: Memorial University. St.John's Nfld, Canada Lines: 1 Please delete my subscription. From owner-rapd@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: List of UBC primers Message-ID: <455BCAF2CA9@uamercury.uark.edu> Date: 9 Sep 93 21:19:13 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 710 Since others have posted the list of Operon primers I would like to contribute the list of UBC primers. I can't guarantee they all are correct as supplied by John Hobbs but the students in my lab tried to get them entered correctly. 1 CCTGGGCTTC 2 CCTGGGCTTG 3 CCTGGGCTTA 4 CCTGGGCTGG 5 CCTGGGTTCC 6 CCTGGGCCTA 7 CCTGGGGGTT 8 CCTGGCGGTA 9 CCTGCGCTTA 10 GGGGGGATTA 11 CCCCCCTTTA 12 CCTGGGTCCA 13 CCTGGGTGGA 14 CCTGGGTTTC 15 CCTGGGTTTG 16 GGTGGCGGGA 17 CCTGGGCCTC 18 GGGCCGTTTA 19 GCCCGGTTTA 20 TCCGGGTTTG 21 ACCGGGTTTC 22 CCCTTGGGGG 23 CCCGCCTTCC 24 ACAGGGGTGA 25 ACAGGGCTCA 26 TTTGGGCCCA 27 TTTGGGGGGA 28 CCGGCCTTAA 29 CCGGCCTTAC 30 CCGGCCTTAG 31 CCGGCCTTCC 32 GGGGCCTTAA 33 CCGGCTGGAA 34 CCGGCCCCAA 35 CCGGGGTTAA 36 CCCCCCTTAG 37 CCGGGGTTTT 38 CCGGGGAAAA 39 TTAACCGGGC 40 TTACCTGGGC 41 TTAACCGGGG 42 TTAACCCGGC 43 AAAACCGGGC 44 TTACCCCGGC 45 TTAACCCCGG 46 TTAAGGGGGC 47 TTCCCCAAGC 48 TTAACGGGGA 49 TTCCCCGAGC 50 TTCCCCGCGC 51 CTACCCGTGC 52 TTCCCGGAGC 53 CTCCCTGAGC 54 GTCCCAGAGC 55 TCCCTCGTGC 56 TGCCCCGAGC 57 TTCCCCGAGG 58 TTCCCGGAGC 59 TTCCGGGTGC 60 TTGGCCGAGC 61 TTCCCCGACC 62 TTCCCCGTCG 63 TTCCCCGCCC 64 GAGGGCGGGA 65 AGGGGCGGGA 66 GAGGGCGTGA 67 GAGGGCGAGC 68 GAGCTCGCGA 69 GAGGGCAAGA 70 GGGCACGCGA 71 GAGGGCGAGG 72 GAGCACGGGA 73 GGGCACGCGA 74 GAGCACCTGA 75 GAGGTCCAGA 76 GAGCACCAGT 77 GAGCACCAGG 78 GAGCACTAGC 79 GAGCTCGTGT 80 GTGCTCTAGA 81 GAGCACGGGG 82 GGGCCCGAGG 83 GGGCTCGTGG 84 GGGCGCGAGT 85 GTGCTCGTGC 86 GGGGGGAAGG 87 GGGGGGAAGC 88 CGGGGGATGG 89 GGGGGCTTGG 90 GGGGGTTAGG 91 GGGTGGTTGC 92 CCTGGGCTTT 93 GGGGGGAAAG 94 GGGGGGAACC 95 GGGGGGTTGG 96 GGCGGCATGG 97 ATCTGCGAGC 98 ATCCTGCCAG 99 ATCCCCTGGG 100 ATCGGGTCCG 101 GCGGCTGGAG 102 GGTGGGGACT 103 GTGACGCCGC 104 GGGCAATGAT 105 CTCGGGTGGG 106 CGTCTGCCCG 107 CTGTCCCTTT 108 GTATTGCCCT 109 TGTACGTGAC 110 TAGCCCGCTT 111 AGTAGACGGG 112 GCTTGTGAAC 113 ATCCCAAGAG 114 TGACCGAGAC 115 TTCCGCGGGC 116 TACGATGACG 117 TTAGCGGTCT 118 CCCGTTTTGT 119 ATTGGGCGAT 120 GAATTTCCCC 121 ATACAGGGAG 122 GTAGACGAGC 123 GTCTTTCAGG 124 ACTCGAAGTC 125 GCGGTTGAGG 126 CTTTCGTGCT 127 ATCTGGCAGC 128 GCATATTCCG 129 GCGGTATAGT 130 GGTTATCCTC 131 GAAACAGCGT 132 AGGGATCTCC 133 GGAAACCTCT 134 AACACACGAG 135 AAGCTGCGAG 136 TACGTCTTGC 137 GGTCTCTCCC 138 GCTTCCCCTT 139 CCCAATCTTC 140 GTCGCATTTC 141 ATCCTGTTCG 142 ATCTGTTCGG 143 TCGCAGAACG 144 AGAGGGTTCT 145 TGTCGGTTGC 146 ATGTGTTGCG 147 GTGCGTCCTC 148 TGTCCACCAG 149 AGCAGCGTGG 150 GAAGGCTCTG 151 GCTGTAGTGT 152 CGCACCGCAC 153 GAGTCACGAG 154 TCCATGCCGT 155 CTGGCGGCTG 156 GCCTGGTTGC 157 CGTGGGCAGG 158 TAGCCGTGGC 159 GAGCCCGTAG 160 CGATTCAGAG 161 CGTTATCTCG 162 AACTTACCGC 163 CCCCCCAGAT 164 CCAAGATGCT 165 GAAGGCACTG 166 ACTGCTACAG 167 CCAATTCACG 168 CTAGATGTGC 169 ACGACGTAGG 170 ATCTCTCCTG 171 TGACCCCTCC 172 ACCGTCGTAG 173 CAGGCGGCGT 174 AACGGGCAGC 175 TGGTGCTGAT 176 CAAGGGAGGT 177 TCAGGCAGTC 178 CCGTCATTGG 179 TCACTGTACG 180 GGGCCACGCT 181 ATGACGACGG 182 GTTCTCGTGT 183 CGTGATTGCT 184 CAAACGGCAC 185 GTGTCTTCAC 186 GTGCGTCGCT 187 AACGGGGGAG 188 GCTGGACATC 189 TGCTAGCCTC 190 AGAATCCGCC 191 CGATGGCTTT 192 GCAAGTCACT 193 TGCTGGCTTT 194 AGGACGTGCC 195 GATCTCAGCG 196 CTCCTCCCCC 197 TCCCCGTTCC 198 GCAGGACTGC 199 GCTCCCCCAC 200 TCGGGATATG 201 CTGGGGATTT 202 GAGCACTTAC 203 CACGGCGAGT 204 TTCGGGCCGT 205 CGGTTTGGAA 206 GAGGACGTCC 207 CATATCAGGG 208 ACGGCCGACC 209 TGCACTGGAG 210 GCACCGAGAG 211 GAAGCGCGAT 212 GCTGCGTGAC 213 CAGCGAACTA 214 CATGTGCTTG 215 TCACACGTGC 216 CATAGACTCC 217 ACAGGTAGAC 218 CTCAGCCCAG 219 GTGACCTCAG 220 GTCGATGTCG 221 CCCGTCAATA 222 AAGCCTCCCC 223 GATCCATTGC 224 TCTCCGGTAT 225 CGACTCACAG 226 GGGCCTCTAT 227 CTAGAGGTCC 228 GCTGGGCCGA 229 CCACCCAGAG 230 CGTCGCCCAT 231 AGGGAGTTCC 232 CGGTGACATC 233 CTATGCGCGC 234 TCCACGGACG 235 CTGAGGCAAA 236 ATCGTACGTG 237 CGACCAGAGC 238 CTGTCCAGCA 239 CTGAAGCGGA 240 ATGTTCCAGG 241 GCCCGACGCG 242 CACTCTTTGC 243 GGGTGAACCG 244 CAGCCAACCG 245 CGCGTGCCAG 246 TATGGTCCGG 247 TACCGACGGA 248 GAGTAAGCGG 249 GCATCTACCG 250 CGACAGTCCC 251 CTTGACGGGG 252 CTGGTGATGT 253 CCGTGCAGTA 254 CGCCCCCATT 255 TTCCTCCGGA 256 TGCAGTCGAA 257 CGTCACCGTT 258 CAGGATACCA 259 GGTACGTACT 260 TCTCAGCTAC 261 CTGGCGTGAC 262 CGCCCCCAGT 263 TTAGAGACGG 264 TCCACCGAGC 265 CAGCTGTTCA 266 CCACTCACCG 267 CCATCTTGTG 268 AGGCCGCTTA 269 CCAGTTCGCC 270 TGCGCGCGGG 271 GCCATCAAGA 272 AGCGGGCCAA 273 AATGTCGCCA 274 GTTCCCGAGT 275 CCGGGCAAGC 276 AGGATCAAGC 277 AGGAAGGTGC 278 GGTTCCAGCT 279 AGACATTAGA 280 CTGGGAGTGG 281 GAGAGTGGAA 282 GGGAAAGCAG 283 CGGCCACCGT 284 CAGGCGCACA 285 GGGCGCCTAG 286 CGGAGCCGGC 287 CGAACGGCGG 288 CCTCCTTGAC 289 ATCAAGCTGC 290 CCGCGAGCAC 291 AGCTGAAGAG 292 AAACAGCCCG 293 TCGTGTTGCT 294 TGATTGGCCA 295 CGCGTTCCTG 296 CCGCTGGGAG 297 GCGCATTAGA 298 CCGTACGGAC 299 TGTCAGCGGT 300 GGCTAGGGCG 301 CGGTGGCGAA 302 CGGCCCACGT 303 GCGGGAGACC 304 AGTCCTCGCC 305 GCTGGTACCC 306 GTCCTCGTAG 307 CGCATTTGCA 308 AGCGGCTAGG 309 ACATCCTGCG 310 GAGCCAGAAG 311 GGTAACCGTA 312 ACGGCGTCAC 313 ACGGCAGTGG 314 ACTTCCTCCA 315 GGTCTCCTAG 316 CCTCACCTGT 317 CTAGGGGCTG 318 CGGAGAGCGA 319 GTGGCCGCGC 320 CCGGCATAGA 321 ATCTAGGGAC 322 GCCGCTACTA 323 GACATCTCGC 324 ACAGGGAACG 325 TCTAAGCTCG 326 CGGATCTCTA 327 ATGGCCTTAC 328 ATGGCCTTAC 329 GCGAACCTCC 330 GGTGGTTTCC 331 GCCTAGTCAC 332 AACGCGTAGA 333 GAATGCGACG 334 ATGGCAAAGC 335 TGGACCACCC 336 GCCACGGAGA 337 TCCCGAACCG 338 CTGTGGCGGT 339 CTCACTTGGG 340 GAGAGGCACC 341 CTGGGGCCGT 342 GAGATCCCTC 343 TGTTAGGCTC 344 TGTTAGGCAC 345 GCGTGACCCG 346 TAGGCGAACG 347 TTGCTTGGCG 348 CACGGCTGCG 349 GGAGCCCCCT 350 TGACGCGCTC 351 CTCCCGGTGG 352 CACAACGGGT 353 TGGGCTCGCT 354 CTAGAGGCCG 355 GTATGGGGCT 356 GCGGCCCTCT 357 AGGCCAAATG 358 GGTCAGGCCC 359 AGGCAGACCT 360 CTCTCCAGGC 361 GCGAGGTGCT 362 CCGCCTTACA 363 ATGACGTTGA 364 GGCTCTCGCG 365 TAGACAGAGG 366 CCTGATTGCC 367 ACCTTTGGCT 368 ACTTGTGCGG 369 GCGCATAGCA 370 TCAGCCAGCG 371 TCTCGATTGC 372 CCCACTGACG 373 CTGAGGAGTG 374 GGTCAACCCT 375 CCGGACACGA 376 CAGGACATCG 377 GACGGAAGAG 378 GACAACAGGA 379 GGGCTAGGGT 380 AGGAGTGAGA 381 ATGAGTCCTG 382 ATACACCAGC 383 GAGGCGCTGC 384 TGCGCCGCTA 385 ACCGGGAACG 386 TGTAAGCTCG 387 CGCTGTCGCC 388 CGGTCGCGTC 389 CGCCCGCAGT 390 TCACTCAGAG 391 GCGAACCTCG 392 CCTGGTGGTT 393 TTCCATGCCT 394 TCACGCAGTT 395 TCACTTGAGG 396 GAATGCGAGG 397 GGGCTGTGCC 398 CAGTGCTCTT 399 TTGCTGGGCG 400 GCCCTGATAT 401 TAGGACAGTC 402 CCCGCCGTTG 403 GGAAGGCTGC 404 TCTCTACGAC 405 CTCTCGTGCG 406 GCCACCTCCT 407 TGGTCCTGGC 408 CCGTCTCTTT 409 TAGGCGGCGG 410 CGTCACAGAG 411 GAGGCCCGTT 412 TGCGCCGGTG 413 GAGGCGGCGA 414 AAGGCACCAG 415 GTTCCAGCAG 416 GTGTTTCCGG 417 GACAGGCCAA 418 GAGGAAGCTT 419 TACGTGCCCG 420 GCAGGGTTCG 421 ACGGCCCACC 422 CACCTGCGGG 423 GGGTCTCGAA 424 ACGGAGGTTC 425 CGTCGGGCCT 426 TCTCCCGGTG 427 GTAATCGACG 428 GGCTGCGGTA 429 AAACCTGGAC 430 AGGCGGCACC 431 CTGCGGGTCA 432 AGCGTCGACT 433 TCACGTGCCT 434 TCGCTAGTCC 435 CTAGTAGGGG 436 GAGGGGGCCA 437 AGTCCGCTGC 438 AGACGGCCGG 439 GCCCCTTGAC 440 CTGTCGAACC 441 CTGCTGTCTT 442 CTACTCGGTT 443 TGATTGCTCG 444 GCAGCCCCAT 445 TAGCAGCTTG 446 GCCAGCGTTC 447 CAGGCTCTAG 448 GTTGTGCCTG 449 GAGGTTCAAC 450 CGGAGAGCCC 451 CTAATCTCGC 452 CTAATCACGG 453 AGTACAAGGG 454 GCTTACGGCA 455 AGCAAGCCGG 456 GCGGAGGTCC 457 CGACGCCCTG 458 CTCACATGCC 459 GCGTCGAGGG 460 ACTGACCGGC 461 CCCGTATGTC 462 CATAGCGGCA 463 AGGCGGAAGC 464 CACAAGCCTG 465 GGTCAGGGCT 466 TTCTTAGCGG 467 AGCACGGGCA 468 ACGGAAGCGC 469 CTCCAGCAAA 470 AGGAGCTGGG 471 CCGACCGGAA 472 AGGCGTGCAA 473 ATCCCCAAGA 474 AGGCGGGAAC 475 CCAGCGTATT 476 TTGAGGCCCT 477 TGTTGTGCCC 478 CGAGCTGGTC 479 CTCATACGCG 480 GGAGGGGGGA 481 GTAATTGCGC 482 CTATAGGCGG 483 GCACTAAGAC 484 CTGGCAAGGA 485 AGAATAGGGC 486 CCAGCATCAG 487 GTGGCTAGGT 488 TTCGCTTCTC 489 CGCACGCACA 490 AGTCGACCTT 491 TCCTGTCAAG 492 GTGACTGCTC 493 CCGAATCACT 494 TGATGCTGTC 495 CTTTCCTTCC 496 CCTTTCAAGG 497 GCATAGTGCG 498 GACAGTCCTG 499 GGCCGATGAT 500 TTGCGTCATG 501 CGGATATACC 502 GCATGGTAGC 503 ATCGTCCAAC 504 ACCGTGCGTC 505 CCCTTTACAC 506 CCTTTCCCGA 507 AGACGTACTC 508 CGGGGCGGAA 509 ACAGAGACTG 510 CGCATCTCTT 511 GAATGGTGAG 512 GGGTGGACAT 513 TATACGACCC 514 CGGTTAGACG 515 GGGGGCCTCA 516 AGCGCCGACG 517 GGTCGCAGCT 518 TGCTGGTCCA 519 ACCGGACACT 520 TGCGCAGCCC 521 CCGCCCCACT 522 TCGTCTAGCA 523 ACAGGCAGAC 524 CGGTTACTAG 525 GCTGGTTGGA 526 AACGGGCACC 527 CTTCAACGTG 528 GGATCTATGC 529 CACTCCTACA 530 AATAACCGCC 531 GCTCACTGTT 532 TTGAGACAGG 533 GCATCTACGC 534 CACCCCCTGC 535 CCACCAACAG 536 GCCCCTCGTC 537 CGAAAGGACT 538 TGACCTCTCC 539 CTTACGTCAC 540 CGGACCGCGT 541 GCCCCTTTAC 542 CCCATGGCCC 543 CGCTTCGGGT 544 TAGAGACTCC 545 ACGTTGAGAC 546 CCCGCAGAGT 547 TATGACCTGG 548 GTACATGGGC 549 CCGGCTTATG 550 GTCGCCTGAG 551 GGAAGTCCAC 552 CTAAATGGCG 553 TTCGAGATCG 554 TCATCCAGGG 555 GTGAACAGCA 556 ATGGATGACG 557 GTGTAGAGCC 558 CGATATCCGG 559 GAGAACTGGC 560 CACTGCTGTC 561 CATAACGACC 562 CAAAGTAGCC 563 CGCCGCTCCT 564 CGGCGTTACG 565 GGTCGATTTC 566 CCACATGCGA 567 ACCTGTTCTC 568 ACCTGTTCTC 569 CGAATTGCTG 570 GGCCGCTAAT 571 GCGCGGCACT 572 TTCGACCATC 573 CCCTAATCAG 574 GCCAGACAAG 575 GGAGATGTAC 576 CACCTAATGG 577 GTCTGATGTG 578 GGTGTCCACT 579 TGGAATCGTG 580 GCGATAGTCC 581 CCCGTTAAGG 582 GGTATAGACG 583 GTATTTGCGC 584 GCGGGCAGGA 585 CCCGCGAGTC 586 CCGGTTCCAG 587 GCTACTAACC 588 CAGAGGTTGG 589 GACGGAGGTC 590 CCGGCATGTT 591 TCCCTCGTGG 592 GGGCGAGTGC 593 CGAGCTTTGA 594 AGGAGCTGGC 595 GTCACCGCGC 596 CCCCTCGAAT 597 TGGTTCCCGA 598 ACGGGCGCTC 599 CAAGAACCGC 600 GAAGAACCGC 601 CCGCCCACTG 602 GCGAAGACTA 603 ACCCACCGCG 604 GGCCCATTGC 605 CCGATCATTC 606 CGGTCGGCCA 607 AGTGTCGTCG 608 GAGCCCGAAA 609 ACAGCACCAT 610 TTTGCCGCCC 611 CCATCGTACC 612 CCGTGAGTAT 613 TGCACCCACG 614 GTAGTCTCGC 615 CGTCGAGCGG 616 CGGAAGAAAC 617 CGGACTATGT 618 CGGACTATGT 619 TTCCCTAGCG 620 TTGCGCCCGG 621 GTCTGCGCTA 622 ACAGGTGGTT 623 TGCGGGACTG 624 GTGATAAGCC 625 CCGCTGGAGC 626 CCAAGCCCGG 627 GGATTCACAG 628 GTCTGGTTAG 629 GCAAGTATGC 630 CACTCTCTGG 631 GGCTTAACCG 632 GAGTTTACCC 633 CTGTGTATCC 634 CCGTACACGC 635 CTCAGCTCAG 636 GGGATATCGC 637 CCCTAAAGCG 638 GCGGTGACTA 639 ATCGAGCACC 640 CGTGGGGCCT 641 TGGAACCATG 642 GTGGTCTCGA 643 ATAAGCGGTG 644 TCGTATTGGG 645 TACAGCGTTG 646 GTCCACTTCC 647 CCTGTGGGGG 648 GCACGCGAGA 649 AATGCTGGAC 650 AGTATGCAGC 651 TCATTTCGCC 652 CCCAACACAC 653 CATGCAAGAC 654 CCCTGGTCTG 655 GCATTTCCCG 656 CGTAACCTTG 657 GTCCTTTAGC 658 CCTATGTACC 659 CGGTTTCGTA 660 AGACGCCGAC 661 CCTGCTTACG 662 GGCTACGTCT 663 CGTATAGCCG 664 GCCTGAAAAC 665 GACGCTTTTC 666 CTTAACACGC 667 CGCAGAAATC 668 CCCGATTGAG 669 GTTACACCAC 670 CCCTTGAGAC 671 CATTAAGGCG 672 TACCGTGGCG 673 TTCATACGCG 674 ATCGATCCGG 675 ACCGGTGGAG 676 GCTAACGTCC 677 TCTCAGGACA 678 AGCGGAGCTG 679 GATGGGGTGG 680 AATGAGAGCC 681 CCCCCGGACT 682 CTGCGACGGT 683 TATTACCGCC 684 CCACACGTAG 685 GATCGCAGGC 686 CGTGACAGGA 687 ATACAAGGGG 688 GCAGGAGCGT 689 TGTCCGGAAG 690 TAATCCGGTC 691 AAACCAGGCG 692 ACATTGGGGG 693 GACGAGACGG 694 GGTTTGGAGG 695 GCTAATCAGC 696 CGGACATGGC 697 CGCAGGTCAC 698 CTAGACGTTG 699 GTTACTGCCC 700 GGACTAAGGT Doug Rhoads || Dept. of Biological Sciences drhoads@mercury.uark.edu || 601 Science Engineering drhoads@uafsysb.uark.edu || University of Arkansas 501-575-3251 || Fayetteville, AR 72701 From owner-rapd@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!spool.mu.edu!umn.edu!gaia.ucs.orst.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein3.u.washington.edu!toby From: toby@stein3.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Bad Falcon 3911 96-well plates in MJ thermocycler Message-ID: <26obsc$2e7@news.u.washington.edu> Date: 9 Sep 93 22:48:44 GMT Organization: University of Washington Lines: 23 NNTP-Posting-Host: stein.u.washington.edu Our RAPDs crashed recently, and in the hair-pulling that followed we traced the problem to the Falcon 3911 96-well PVC plates we are using in our MJ thermocyclers. We checked buffers, dNTPs, primers, templates, water, oil, Taq, and even took extra care to wash our plates thoroughly (we always wash them before using, as many lots of plates will give spotty results unless this is done) before identifying the culprit. By using 1.5ml Eppendorf tubes in the temp block (they will stand there by themselves even in the 96-well format) we found that the other reagents were OK. We have many lots of Falcon 3911 plates, and most other lots worked fine (although none worked quite as well as tubes). The real bad lot of plates would give some PCR products when locus-specific primers were used with short denaturation times (15"), but would give absolutely zip with the standard RAPD cycle conditions (94x1'/36x1'/72x2' X 35). Perhaps the longer time at high temps drives some plasticizer out of this lot of plates that poisons the reaction. Unfortunately, the Falcon plates do not have the lot numbers on each dispenser, only on the cardboard shipping box, so I can't tell you which lot number to avoid. Just one more thing to screw up in an already screwy system :) -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!poplar1.cfr.washington.edu From: cgr@poplar1.cfr.washington.edu (carl g. riches) Newsgroups: bionet.agroforestry,bionet.molbio.rapd,bionet.announce,bionet.general,bionet.plants Subject: Poplar Molecular Network Gopher Server Keywords: poplar molecular biology genetics gopher Message-ID: <26oend$s51@news.u.washington.edu> Date: 9 Sep 93 23:37:17 GMT Sender: kristoff@net.bio.net Reply-To: cgr@poplar1.cfr.washington.edu Organization: University of Washington Lines: 24 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.agroforestry:375 bionet.molbio.rapd:221 bionet.announce:693 bionet.general:6006 bionet.plants:1742 The Poplar Molecular Network (PMN) now has a gopher server providing information for persons interested in the molecular nature of _Populus_ species, and poplar and cottonwood research. .Link information: Name=Poplar Molecular Network Gopher Port=70 Host=poplar1.cfr.washington.edu Contents: PMN Newsletter Genetic Linkage Maps Laboratory Protocols links to some bioscience gophers for further information, or in case of problems, send e-mail to: dbadmin@poplar1.cfr.washington.edu --- carl g. riches college of forest resources internet: cgr@poplar1.cfr.washington.edu university of washington ar-10 voice: 206-543-2764 seattle, wa 98195 fax: 206-543-3254 From owner-rapd@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Common Sequences UBC vs. Operon Message-ID: <26ocjq$drh@overload.lbl.gov> Date: 9 Sep 93 23:01:14 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 13 NNTP-Posting-Host: s27w007.pswfs.gov Based on the data posted to this group by Bradshaw and Hobbs the only common sequence between the Operon kits and the UBC kits is: AGGCGGGAAC UBC-478 OPL-07 --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!SOL.CCS.DEAKIN.EDU.AU!huangbx From: huangbx@SOL.CCS.DEAKIN.EDU.AU ("Huang Bixing") Newsgroups: bionet.molbio.rapd Subject: Random primers for abalone RAPD Message-ID: <58200.huangbx@mail-g.deakin.EDU.AU> Date: 10 Sep 93 21:09:49 GMT Sender: daemon@net.bio.net Reply-To: Distribution: bionet Lines: 19 Hello all, There are quite a few random primer sequences available from UBC and Operon. Could anyone be kindly to help me to decide what primers I should choose for abalone RAPD? Any suggestions will be very appreciated! Thank you. Bixing Huang Department of Biology Deakin University Email: huangbx.deakin.EDU.AU ----- School of Biological and Chemical Sciences, Deakin University, Geelong ----- From owner-rapd@net.bio.net Fri Sep 10 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!gatech!howland.reston.ans.net!spool.mu.edu!think.com!hsdndev!nmr-z!Frodo.MGH.Harvard.EDU!FINNEY From: finney@Frodo.MGH.Harvard.EDU (Michael Finney) Newsgroups: bionet.molbio.rapd Subject: Re: Bad Falcon 3911 96-well plates in MJ thermocycler Message-ID: <1993Sep10.221103.421@nmr-z.mgh.harvard.edu> Date: 10 Sep 93 22:11:03 GMT References: <26obsc$2e7@news.u.washington.edu> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: finney@Frodo.MGH.Harvard.EDU Organization: Molecular Biology, Massachusetts General Hospital Lines: 23 Nntp-Posting-Host: frodo.mgh.harvard.edu In article <26obsc$2e7@news.u.washington.edu>, toby@stein3.u.washington.edu (Toby Bradshaw) writes: >Our RAPDs crashed recently, and in the hair-pulling that followed >we traced the problem to the Falcon 3911 96-well PVC plates we are >using in our MJ thermocyclers. ... >Perhaps >the longer time at high temps drives some plasticizer out of >this lot of plates that poisons the reaction. Chemicals from the plates may well be one problem, but there is at least one other problem with the plates. These plates were actually designed to bind high levels of protein. The result is that they can bind and inactivate enzymes used in them. Most people put some kind of blocking protein (gelatin, BSA) in their reaction mixes, but it may not be enough for all batches of plates. An alternative is to pre-block the plates with 100 micrograms/ml BSA. Two other companies make equivalent plates, Dynatech and Costar. If there are too many problems with Falcon, you could switch (or threaten to switch) brands. As far as I know there is no great difference in quality among the three. Mike From owner-rapd@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!news.ans.net!malgudi.oar.net!chemabs!ljc55 From: ljc55@cas.org (Linda J. Carter) Newsgroups: bionet.molbio.rapd Subject: PCR primers and hybridization probes Keywords: biosequence database PCR primer and hybridization probe Message-ID: <1993Sep13.174656.21751@cas.org> Date: 13 Sep 93 17:46:56 GMT References: <455BCAF2CA9@uamercury.uark.edu> Sender: usenet@cas.org Reply-To: ljc55@cas.org Organization: Chemical Abstracts Service Lines: 27 For those of you interested in PCR primers and hybridization probes I would really appreciate your opinions about their inclusion in biosequence databases. Some of my specific concerns are as follows: 1. Do you feel primers and probes tend to clutter up a nucleic acid database and cause unnecessary retrievals when searching for sequences of much longer length? 2. Because primers and probes are usually designed from known sequence information often already in the database, is it still justifiable to include them as additional entries? 3. What applications of primers and probes should justify their inclusion in a biosequence database, e.g. clinical diagnosis, taxonomy, evolution, gene mapping, or methods? 4. If you were to search for primers and probes in a biosequence database what would be most efficient for you? Would some type of descriptive information be helpful, e.g. their application or their origin? Thank you very much for any thoughts you might have on this subject. Please post your response to ljc55@cas.org From owner-rapd@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!torn!csd.unb.ca!news.ucs.mun.ca!kean.ucs.mun.ca!gchen From: gchen@kean.ucs.mun.ca Newsgroups: bionet.molbio.rapd Subject: discuss about subtraction Message-ID: <1993Sep12.215323.1@kean.ucs.mun.ca> Date: 13 Sep 93 01:23:23 GMT Sender: usenet@news.ucs.mun.ca (NNTP server account) Organization: Memorial University. St.John's Nfld, Canada Lines: 5 Does anybody know a novel method about buliding subtractive cDNA library from small amount of mRNA ? Also I am interested at any methods which can be used to identify differentially expressed genes ( i.e. something animating plus and minus screening ). Thanks in advance! From owner-rapd@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!emory!nigel.msen.com!fmsrl7!lynx.unm.edu!triton.unm.edu!news-user From: dkim@unm.edu Newsgroups: bionet.molbio.rapd Subject: Re: discuss about subtraction Message-ID: <272cbs$j2n@triton.unm.edu> Date: 13 Sep 93 17:58:20 GMT References: <1993Sep12.215323.1@kean.ucs.mun.ca> Sender: kim@flovax.lanl.gov (Daniel Kim) Organization: University of New Mexico, Albuquerque Lines: 13 NNTP-Posting-Host: triton.unm.edu I don't really understand what RAPD's are. They seem to be a PCR reaction on whole DNA using short arbitrary primers. If this is the case, then differential gene expression can be determined in a similar way using the Differential Display PCR method of Liang and Pardee (Sorry, forgot the citation) or a variation of McClelland, et.al. Nucl. Acids. Res. 20:4965-4970. I'm trying the McClelland method on plant RNA, with no success so far, but the use of plant RNA is problematic in terms of purification of template. Does anyone here have any suggestions re:differential display-like procedures? Thanks Daniel Kim From owner-rapd@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!zaphod.crihan.fr!univ-lyon1.fr!ghost.dsi.unimi.it!batcomputer!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!stein2.u.washington.edu!toby From: toby@stein2.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <27558d$3q4@news.u.washington.edu> Date: 14 Sep 93 19:15:25 GMT References: <2751ui$3l4@overload.lbl.gov> Organization: University of Washington, Seattle Lines: 21 NNTP-Posting-Host: stein.u.washington.edu In article <2751ui$3l4@overload.lbl.gov>, Bradley K. Sherman wrote: >I would like to make a suggestion w.r.t. publishing RAPD genetic >maps. Why not name the loci using the explicit 10-mer plus >the molecular weight of the band (if appropriate) in basepairs? > > ggactaaggt-811 is a fully informative name for a RAPD locus. In a given pedigree it may be fully informative, but would not necessarily translate across pedigrees. This is not a problem for maps generated from haploid tissue or full-sib diploid families. Also, the length of the product is not generally known with such precision. In principle, there's no reason not to use this nomenclature, though Operon might prefer to see its initials used for loci detected with its primers :) >Admittedly this does not scale well, but it should be okay up >to about 16 basepairs. The legend for the map can contain the >source of the primers. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: H.F.J.Bligh@uk.ac.nottingham.ccc.vme Newsgroups: bionet.molbio.rapd Subject: re:subtraction Message-ID: <1993Sep14.074922.10635@gserv1.dl.ac.uk> Date: 14 Sep 93 07:50:47 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Precedence: first-class Original-To: rapd@uk.ac.daresbury I've also been doing a sort of differential display using plant material. A few months back I put in a posting about this because my boss had given me a very woolly description of it and I couldn't find it in the literature (wrong keywords it turned out!). Anyway, while all the lovely netters out there were posting me the info I was looking for I meanwhile cobbled together a method of my own. Basically you take your RNA and do a reverse transcriptase reaction priming with random hexamers or pentamers then you use this reaction to set up a whole load of RAPD reactions. I got some raelly nice results with clonable bands which confirmed that it really*was* tissue specific. re Daniels problem with template, I found that leaf was a piece of cake but seed is distinctly more problematic and I had to purify the polyA fraction after which it worked really nicely. Hope this helps people and sparks off some discussion , which is what we're here for , after all. cheers Frankie From owner-rapd@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: A modest proposal for naming RAPD loci Message-ID: <2751ui$3l4@overload.lbl.gov> Date: 14 Sep 93 18:18:58 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 18 NNTP-Posting-Host: s27w007.pswfs.gov I would like to make a suggestion w.r.t. publishing RAPD genetic maps. Why not name the loci using the explicit 10-mer plus the molecular weight of the band (if appropriate) in basepairs? ggactaaggt-811 is a fully informative name for a RAPD locus. Admittedly this does not scale well, but it should be okay up to about 16 basepairs. The legend for the map can contain the source of the primers. --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: bertheau@fr.inra.inapg.inapv (Yves Bertheau) Newsgroups: bionet.molbio.rapd Subject: SIGNOFF RAPD-L Message-ID: <1993Sep15.171153.21677@gserv1.dl.ac.uk> Date: 15 Sep 93 18:11:22 GMT Sender: bertheau@inapv.inapg.inra.fr Distribution: bionet Lines: 15 Precedence: first-class Original-To: rapd@uk.ac.daresbury Pp-Warning: Illegal Received field on preceding line Original-Received: by inapv.inapg.inra.fr, Wed, 15 Sep 93 19: 11:23 +0100 X-Mailer: ELM [version 2.2 PL7] Could you unsubscribe me of the rapd-l list. I am now using the bionet.molbio.rapd forum. Thank you -- Yves Bertheau INRA INA P-G Pathologie Vegetale 16 rue Claude Bernard 75231 Paris cedex 05 FRANCE Phone: +33 (1) 44.08.1704 +33 (1) 44.08.16.98 Fax : +33 (1) 44.08.17.00 Telex: 250985 Internet: bertheau@inapv.inapg.inra.fr From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!europa.eng.gtefsd.com!howland.reston.ans.net!spool.mu.edu!uwm.edu!rpi!batcomputer!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!stein3.u.washington.edu!toby From: toby@stein3.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <2782hg$rp7@news.u.washington.edu> Date: 15 Sep 93 21:47:28 GMT References: <2751ui$3l4@overload.lbl.gov> <27558d$3q4@news.u.washington.edu> <277tle$bvq@overload.lbl.gov> Organization: University of Washington, Seattle Lines: 29 NNTP-Posting-Host: stein.u.washington.edu In article <277tle$bvq@overload.lbl.gov>, Dave Harry wrote: On the precision of MW estimates and (presumptive) homology of RAPDs >These strike me as related problems. The sad truth, however (and please >correct me if you feel otherwise) is that with RAPDs there is little that >might translate across pedigrees. For some specialized pedigrees, like the F2s of interspecific hybrids I have worked on, RAPDs do seem to likely to translate across pedigrees. This is a result of the two species in question becoming fixed or nearly fixed for alternate RAPD alleles at many loci. Hence, these RAPDs should map at the same relative position in all such interspecific F2s. In the case of Populus trichocarpa x P. deltoides, two tree species with high levels of genetic diversity and individual heterozygosity, we found that about 40% of the RAPDs mapped in our F2 were essentially fixed in one species or the other. Our test for fixation was not rigorous, containing only about 10 members of each species. Operationally for us in our mapping, "fixation" only means that all 10 of one species had the band and all 10 of the other lacked the band, so the frequency of the "with-band" allele could be considerably less than 1 and still appear in all 10 of one species. Nevertheless, it would seem that a high proportion of RAPDs in interspecific F2s might be conserved in map position, making a framework map of RAPDs feasible in this special case. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!agate!overload.lbl.gov!deh From: deh@s27w007.pswfs.gov (Dave Harry) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <277tle$bvq@overload.lbl.gov> Date: 15 Sep 93 20:24:14 GMT References: <2751ui$3l4@overload.lbl.gov> <27558d$3q4@news.u.washington.edu> Organization: Dendrome, A Genome Database for Forest Trees Lines: 25 NNTP-Posting-Host: s27w007.pswfs.gov >>the molecular weight of the band (if appropriate) in basepairs? >> >> ggactaaggt-811 is a fully informative name for a RAPD locus. > >In a given pedigree it may be fully informative, but would not necessarily >translate across pedigrees. This is not a problem for maps generated from ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >haploid tissue or full-sib diploid families. Also, the length of the >product is not generally known with such precision. In principle, there's ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ These strike me as related problems. The sad truth, however (and please correct me if you feel otherwise) is that with RAPDs there is little that might translate across pedigrees. What we really mean by this is that a given RAPD fragment has a similar DNA sequence to another, and hence we *presume* this to be homologous. What's necessary to infer this experimentally is to blot and hybridize (as Tingey et al has suggested several times), perhaps with agreed-upon standards. At least a primer name (whatever alphabet is used) and a MW estimate gives some information from which to design subsequent experiments. Dave Harry (while I work with Brad, our opinions are generated on our own!) From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <277ipd$7oj@overload.lbl.gov> Date: 15 Sep 93 17:18:37 GMT References: <9309151401.AA09143@net.bio.net> Distribution: bionet Organization: Dendrome, A Genome Database for Forest Trees Lines: 44 NNTP-Posting-Host: s27w007.pswfs.gov In article <9309151401.AA09143@net.bio.net> T80MAJ1@NIU.BITNET writes: > >My problems with this: > 1. Very easy to accidentally mis-transcribe the > non-intuitive sequence > > 2. Not much fun to use in conversation I cannot respond to objection 2, as one person's conversational fun may be distilled ennui to another. As a database curator, I completely agree with 1. A possible solution is to use a larger alphabet to represent the same sequence. There are 1048576 permutations of 10 character sequences chosen from an alphabet of 4 characters. Note that it only takes 7 characters from the alphabet {0, 1, ..., 9} to represent this number. Therefore we could consider each 10-mer to be a number written in radix 4, say agree on {a,t,c,g} = {0,1,2,3}. Then each locus is a combination of two integers: 1-811 in the revised proposal is the same as aaaaaaaaat-811 in the original. Then we run into the problem of miscalculation instead of mistranscription! So I will stick with my original proposal for *published* maps, at least. Any system is better than no system. I must plead guilty to mistranscription myself! I stated in a different thread that the UBC and Operon primers UBC-478 and OPL-07 were both AGG CGG GAA C In fact it is UBC-474 and OPL-07 that have that sequence. (Thanks to John Hobbs for pointing this out.) Toby Bradshaw is quite right to criticize my use of the phrase "fully informative." --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!HAL.HAHNEMANN.EDU!libby From: libby@HAL.HAHNEMANN.EDU Newsgroups: bionet.molbio.rapd Subject: RE: Bad Falcon 3911 96-well plates in MJ thermocycler Message-ID: <00972932.343B1560.15525@hal.hahnemann.edu> Date: 15 Sep 93 14:21:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 We also have had bad luck with certain lots of 96-well plates. One thing that seems to help is the inclusion of BSA in reaction buffer - almost any tiny amount will protect reaction. Otherwise, when this won't work, we've been resorting to the expensive plates sold by the thermocycler companies (Techne, Hybaid), which are made with different composition.... From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!NIU.BITNET!T80MAJ1 From: T80MAJ1@NIU.BITNET Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <9309151401.AA09143@net.bio.net> Date: 15 Sep 93 14:01:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 15 Bradley K. Sherman suggests that RAPD loci be named by explicitly naming the 10-mer primer and the band's molecular weight: My problems with this: 1. Very easy to accidentally mis-transcribe the non-intuitive sequence 2. Not much fun to use in conversation I think semi-arbitrary names (short) coupled with band sizes and a separate table giving the source and sequences of the primers is more efficient. ---Rick Johns From owner-rapd@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!munnari.oz.au!uniwa!newsman!csuvax1!torban From: torban@csuvax1.csu.murdoch.edu.au (Torban Bennett) Newsgroups: bionet.molbio.rapd Subject: Software for RAPD profiles? Message-ID: <2784jgINN50q@newsman.csu.murdoch.edu.au> Date: 15 Sep 93 22:22:40 GMT Lines: 10 NNTP-Posting-Host: csuvax1.murdoch.edu.au I am trying to track down good software for the RAPD users here on campus. Does anyone one have any info on a program called Linkage, or software that does RAPD profiles and similarity coefficients? Thanks for any info, in the mean time I'll have a hunt around the usual Bio ftp sites. Torban Bennett torban@murdoch.edu.AU Murdoch University, Western Australia. From owner-rapd@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!embl-heidelberg.de!uni-heidelberg!xlink.net!sol.ctr.columbia.edu!spool.mu.edu!agate!overload.lbl.gov!deh From: deh@s27w007.pswfs.gov (Dave Harry) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <278c3l$hls@overload.lbl.gov> Date: 16 Sep 93 00:30:45 GMT References: <27558d$3q4@news.u.washington.edu> <277tle$bvq@overload.lbl.gov> <2782hg$rp7@news.u.washington.edu> Organization: Dendrome, A Genome Database for Forest Trees Lines: 24 NNTP-Posting-Host: s27w007.pswfs.gov >Nevertheless, it would seem that a high proportion of RAPDs in >interspecific F2s might be conserved in map position, making a >framework map of RAPDs feasible in this special case. > >-Toby Bradshaw >toby@u.washington.edu Thanks, Toby, I stand enlightened. In a more general sense, it would seem that we quickly come back to the relative degree of genetic similarity/heterozygosity within vs between "units" (eg cultivars, species, races, or individuals). But getting back to the point of the original post (from Brad Sherman), wouldn't a MW estimate then be helpful in such a case as yours? For instance, let's say someone else crossed Populus deltoides with another poplar (which is often done) and is now constructing a map using the F2s. If the MW and primer name was available, they'd have some reasonable idea (as a start) which of the RAPD fragments they see (and they should see yours, if indeed it's fixed within P. deltoides) are presumptively homologous to theirs. If this fragment also segregates in their pedigree, it ought to help compare maps in different pedigrees (and even across species) would it not? Dave Harry From owner-rapd@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!spool.mu.edu!uwm.edu!rpi!batcomputer!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!stein3.u.washington.edu!toby From: toby@stein3.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <279vth$bmp@news.u.washington.edu> Date: 16 Sep 93 15:14:57 GMT References: <27558d$3q4@news.u.washington.edu> <277tle$bvq@overload.lbl.gov> <2782hg$rp7@news.u.washington.edu> <278c3l$hls@overload.lbl.gov> Organization: University of Washington, Seattle Lines: 33 NNTP-Posting-Host: stein.u.washington.edu In article <278c3l$hls@overload.lbl.gov>, Dave Harry wrote: >In a more general sense, it would seem >that we quickly come back to the relative degree of genetic >similarity/heterozygosity within vs between "units" (eg cultivars, >species, races, or individuals). Agreed. >But getting back to the point of the original post (from Brad Sherman), >wouldn't a MW estimate then be helpful in such a case as yours? For >instance, let's say someone else crossed Populus deltoides with another >poplar (which is often done) and is now constructing a map using the F2s. >If the MW and primer name was available, they'd have some reasonable idea >(as a start) which of the RAPD fragments they see (and they should see >yours, if indeed it's fixed within P. deltoides) are presumptively >homologous to theirs. If this fragment also segregates in their pedigree, >it ought to help compare maps in different pedigrees (and even across >species) would it not? Especially if the linkage relationship among several such markers is conserved across pedigrees, one might have quite a bit of confidence in the presumed homology. In some ways, I would prefer such a demonstration of conserved RAPD locus order to the Southern blot hybridization of RAPD bands to other RAPD bands, since it is at least formally possible that RAPD bands of similar or the same size could be generated from, say, a repeated sequence that is at several or many different loci in any one individual. The repeat unit producing the "with band" phenotype might vary among individuals. I admit that this kind of thing could be so rare as to be insignificant. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!noc.near.net!saturn.caps.maine.edu!maine.maine.edu!keithh From: KEITHH@MAINE.MAINE.EDU (Keith Hutchison) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <93259.121954KEITHH@MAINE.MAINE.EDU> Date: 16 Sep 93 16:19:54 GMT References: <27558d$3q4@news.u.washington.edu> <277tle$bvq@overload.lbl.gov> <2782hg$rp7@news.u.washington.edu> <278c3l$hls@overload.lbl.gov> Organization: University of Maine System Lines: 30 My turn to wade in on the issue. The question is what information is to be transmitted by the name? Using the sequence of the primer, as Brad suggested, gives no information as to the nature of the sequence amplified. It is likely not to be a 100% predictor as to the sequence of the binding site in the template DNA (allowing for mismatch in the early rounds of amplification). The sequence only helps if I want to have my own oligo synthesized to repeat the experiment. Most labs, I suspect, will be using collections of oligos e.g. Operon's or the UBC oligos. In that case, the source designation (Operon or UBC number) would be more informative, and as implied in an earlier response, less prone to typos. Molecular weight approximations would be useful as starting places but co-migration of unrelated fragments is not unheard of, and given the complexity of RAPD banding patterns would likely occur (low probabilty events happen at a very high frequency in molecular genetics). I will gladden Brad's heart and probably raise a bemused smile on Toby's face to say that this may be a situation where an image file for cross-referencing would be useful. Anyhow, from my perspective, the source designation followed by the molecular weight would provide me with the most useful informationon which to proceed. Keith Hutchison |================================| |=============================|Internet: keithh@maine.maine.edu| | Department of Biochemistry, |================================| | Microbiology, and Molecular Biology 207-581-2827 | | The University of Maine | | 5735 Hitchner Hall | | Orono, ME 04469-5735 | |==========================================================| From owner-rapd@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!europa.eng.gtefsd.com!darwin.sura.net!spool.mu.edu!uwm.edu!rpi!batcomputer!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!stein1.u.washington.edu!toby From: toby@stein1.u.washington.edu (Toby Bradshaw) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <27ab7q$fd3@news.u.washington.edu> Date: 16 Sep 93 18:28:10 GMT References: <27558d$3q4@news.u.washington.edu> <2782hg$rp7@news.u.washington.edu> <278c3l$hls@overload.lbl.gov> <93259.121954KEITHH@maine.maine.edu> Organization: University of Washington, Seattle Lines: 17 NNTP-Posting-Host: stein.u.washington.edu In article <93259.121954KEITHH@maine.maine.edu>, Keith Hutchison wrote: >I will gladden Brad's heart and probably raise a bemused >smile on Toby's face to say that this may be a situation where an image >file for cross-referencing would be useful. Smiling bemusedly, I don't see (no pun) much use for the image, since it doeesn't tell you what you really want to know, i.e. whether the two bands are homologous. It doesn't really tell you anything beyond the estimated molecular weight that most of us agree is a useful addendum to the primer name (unless I'm missing something, always a distinct possibility). For automated scoring, the images would be great. We're still in the "eyeball" scoring mode around here. -Toby Bradshaw toby@u.washington.edu From owner-rapd@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!BCRSSU.AGR.CA!WIERSMA From: WIERSMA@BCRSSU.AGR.CA Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <01H30LMTIQ82000YUJ@GW.AGR.CA> Date: 16 Sep 93 17:36:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 34 16-Sep-1993 In response to the nomenclature and related discussion originated by Brad Sherman I would like to throw in the following thought. It appears to me that the identification of a RAPD loci is based on the DNA of the loci itself (and lack of competing sequences in the reaction) and the RAPD primer itself is only a fortuitous requirement for accessing this sequence. Although the 4 to the 9th possiblities for primers suggests that we will have plenty of variability for naming, the truth is that the total number of primers actually in use is less than a few thousand and repeatedly used for other varieties and species. As more RAPD loci are identified in widely varying species the loci names, given using primer and MWs, will soon be used again for non-homologous sequences. Therefore, it would seem to make sense that a short alphanumeric code given for a specific locus in a specific variety and cross- referenced to the primer used (and band MW) would be less-ambiguous in the long run as it would be assumed to be organism dependant. It would also be something that could be remembered from one thought to the next and more fun (read as humanly feasible) to try to bring into human conversation than a ten (or 7) digit value followed by a molecular weight. Regards, Paul Paul A. Wiersma, Ph.D. Agriculture Canada Research Station phone: (604) 494-7711 Summerland, BC fax : (604) 494-0755 Canada V0H 1Z0 Internet: wiersma@bcrssu.agr.ca From owner-rapd@net.bio.net Thu Sep 16 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!saturn.caps.maine.edu!maine.maine.edu!keithh From: KEITHH@MAINE.MAINE.EDU (Keith Hutchison) Newsgroups: bionet.molbio.rapd Subject: Re: A modest proposal for naming RAPD loci Message-ID: <93260.112339KEITHH@MAINE.MAINE.EDU> Date: 17 Sep 93 15:23:38 GMT References: <27558d$3q4@news.u.washington.edu> <2782hg$rp7@news.u.washington.edu> <278c3l$hls@overload.lbl.gov> <93259.121954KEITHH@maine.maine.edu> <27ab7q$fd3@news.u.washington.edu> Organization: University of Maine System Lines: 50 In article <27ab7q$fd3@news.u.washington.edu> Toby Bradshaw wrote: maine.maine.edu> >Smiling bemusedly, I don't see (no pun) much use for the image, >since it doeesn't tell you what you really want to know, i.e. >whether the two bands are homologous. It doesn't really tell >you anything beyond the estimated molecular weight ... I don't entirely agree. It's usefulness, as is true of any of the parameters mentioned so far, is dependent upon the conservation between the genomes in question. If the RAPD band pattern is sufficiently conserved then it will help to know that a 700bp fragment that you may map, and a 700bp fragment that I am trying to map are both the lower band of a doublet that sits between two bright bands and a fuzzy faint one. It's pattern recognition that the human brain is more capable at than computers (just ask people working with karyotyping software). It's a matter of how much information you want before proceeding with sequencing or blotting to confirm the homology. Since we are resolving RAPD fragments with a single nucleotide length difference (acrylamide gels) size may be a less accurate indicator than position in a pattern unless you are measuring fragments to that accuracy. The above information would help in one way to determine whether two labs are working with the same sequence. But the other strategy for determining homology is to look for syntenic relationships in maps. And for help in designing software to search the map databases I find myself leaning back toward Brad Sherman's original suggestion of giving the actual primer sequence and fragment size. This is away from my earlier opinion to using supplier designations. First, it would define the locus in a supplier-independent and lab-independent fashion, and second, would allow for primers that are not part of the standard kits. In the end, it may not be an important issue since I suspect most RAPD markers will be converted to other types of markers, with a more specific definition being possible. For example, loci defined by RAPD markers segregating in interspecific hybrids really only define the locus for one of species. We only assume the locus is present in the parent giving the null allele. To prove its presence we have to make specific primers. Then it is no longer a RAPD marker but a STS. Keith Hutchison |================================| |=============================|Internet: keithh@maine.maine.edu| | Department of Biochemistry, |================================| | Microbiology, and Molecular Biology 207-581-2827 | | The University of Maine | | 5735 Hitchner Hall | | Orono, ME 04469-5735 | |==========================================================| From owner-rapd@net.bio.net Sun Sep 19 23:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!xlink.net!scsing.switch.ch!aristo.tau.ac.il!pc386 From: pc386@ccsg.tau.ac.il (BENNY SHOMER 9238) Newsgroups: bionet.molbio.rapd Subject: Primers database through gopher. Message-ID: <1993Sep20.175019.25120@aristo.tau.ac.il> Date: 20 Sep 93 17:50:19 GMT Sender: usenet@aristo.tau.ac.il (USENET) Organization: Tel-Aviv University Computation Center Lines: 163 X-Newsreader: TIN [version 1.2 PL1] Hello Bionetters. It has been recently suggested that a searchable database of primers for PCR will be set. The basic idea behind this database is that only ___TESTED_&_WORKING___ (!!!) primers should be contained. This may save many valuable planning and working hours, as well as money. We all know that even carefully planned primers fail to operate when it comes down to the tubes... Dan Jacobson from the Johns Hopkins Univ. GDB, and your humble servant, are now working on the establishment of this database as a gopher server. Cited below is the suggested basic form for this database. We now open a discussion regarding the suggested data fields. We are interested in hearing your opinions regarding this form. Please pay attention to the following: 1. This message has been cross posted to several bionet.xxxx groups. It is suggested however, that the thread will be maintained in bionet.molbio. methds-reagnts . This will make it easier to read and respond to everyone's followups. 2. A followup to the newsgroup is prefferred over direct responses in the Email, so as to keep the thread open. If, for any reason you want to contact us directly, Dan's address is: danj@gdb.org, my @ is: pc386@ccsg.tau.ac.il We hope that this thread will be constructive, and that the database will be 'on the air' as soon as possible. Greetings, Dan Jacobson, Benny Shomer. This is the suggested form: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Primer Name: ______________________________ Target Gene: ______________________________________________________________ Species: ___________________________ Direction: { FOR / REV } Matching Primer(s) in this database: _________________________________ Sequence (5' --> 3'): ___________________________ Length: __ Flanking bases ______ to _____ on the target sequence. Product Length (cDNA):_______ Product Length (genomic):_______ {Lengths are in bp, or 0 for inverse PCR, where length is unknown} Restriction Site Added: _____________ Mutation presented at base: __ Special Applications: { Inverse/ RT-PCR/ Sequencing/ Cloning/ Mutation/ / Ligation Mediated} __________________________________________________________________________ __________________________________________________________________________ ******************** Cycle Conditions ********************************* Hot Start: {Yes/No} Initial Denaturation- Temp: __ Time: ____ Denaturation - Temp: __ Time: ____ Annealing - Temp: __ Time: ____ Extension - Temp: __ Time: ____ Number Of Cycles: __ Final Extension - Temp: __ Time: ____ ********************** Buffer Constituents **************************** (This section basically regards non-standard buffer constituents) Reaction Volume (ul): __ Used Standard Buffer Supplied By: _______________ MgCl2 Concentration (mM): __ DMSO Concentration (%): __ Formamide Concentration (%): __ Gelatin Concentration (%): __ dNTP's Concentration (uM): __ Primers Concentration (uM): __ Polymerase Type: ___________ Polymerase Concentration (U/Rxn.): ___ Make: _____________ ************************************************************************** Submitting Author. Name: __________________________________ Institution: ______________________________________________________________ __________________________________________________________________________ Address: _________________________________________________________________ __________________________________________________________________________ E-mail : ________________________________ Fax# : ______________________ References: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ Remarks: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ************************************************************** * Benny Shomer * * Tel-Aviv University * * Sackler School of Medicine, Dept.of Embryology and Teratology* *--------------------------------------------------------------* * Snail: Ramat-Aviv , Tel-Aviv 69978 , Israel. * * E-mail : pc386@ccsg.tau.ac.il * * Tel : 972-3-640-9238 FAX : 972-3-642-2046 * * * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % So Many Computers , So Little Time ... % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-rapd@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!WELL.SF.CA.US!mjbrauer From: mjbrauer@WELL.SF.CA.US ("Matthew J. Brauer") Newsgroups: bionet.molbio.rapd Subject: Subtractive cDNA libraries Message-ID: <93Sep21.140909pdt.14378-4@well.sf.ca.us> Date: 21 Sep 93 21:08:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 In response to gchen@kean.ucs.mun.ca: The important papers for subtr. hyb'n seem to be: Sive & St. John, Nucleic Acids Research 16:22 (1988), and Wang & Brown, PNAS 88:11505-11509 (1991) For differential display, look up Liang & Pardee, in Science (sorry, I have only a preprint, so I don't know when the paper was actually published. We have had very good results with these techniques, starting with relatively small amounts of mammalian mRNA. From owner-rapd@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!usc!cs.utexas.edu!uunet!munnari.oz.au!newsroom.utas.edu.au!medicalsc49h103.med.utas.edu.au!user From: Kath.Nesbitt@plant.utas.edu.au (Michle Sale) Newsgroups: bionet.molbio.rapd Subject: RAPD analysis Message-ID: Date: 21 Sep 93 04:53:57 GMT Followup-To: bionet.molbio.rapd Organization: University of Tasmania Lines: 14 NNTP-Posting-Host: medicalsc49h103.med.utas.edu.au Hi everyone! I'm not sure if i am doing this correctly as this is the forst message that I have ever posted to a News group. Anyway, I would like to know if anyone out there knows of any programmes, for mac preferably (but PC will do), that calculate genetic distance and can accept missing data? I really don't want to trash half my samples or half my primers so if ypu can help, please E-mail me. Thanks in advance Katherine Nesbitt. From owner-rapd@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!YVAX.BYU.EDU!FARMERJ From: FARMERJ@YVAX.BYU.EDU Newsgroups: bionet.molbio.rapd Subject: Re: RAPD analysis Message-ID: <01H37G5CMH9U94FNLM@yvax.byu.edu> Date: 21 Sep 93 16:18:24 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Brigham Young University Lines: 5 You didn't specify what kind of data you are analyzing. If they are sequence data, PHYLIP programs will accept "--" in place of bases. I imagine other programs will do the same, but I haven't used them yet. PHYLIP is available from Joseph Felsenstein at no charge: joe@genetics.washington.edu James Farmer, farmerj@yvax.byu.edu From owner-rapd@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!avdms8.msfc.nasa.gov!sol.ctr.columbia.edu!destroyer!newsrelay.iastate.edu!cobra.uni.edu!jurgenson From: jurgenson@cobra.uni.edu Newsgroups: bionet.molbio.rapd Subject: deepvent pol. Message-ID: <1993Sep23.165639.17051@cobra.uni.edu> Date: 23 Sep 93 21:56:39 GMT Organization: University of Northern Iowa Lines: 8 We are just beginning rapid experiments using two base primers on DNA of Aspergillus nidulans a filmaneous fungi. WE notice that most of the liturature uses taq polymerase for PRPD analysis and would like to know if anyone has used DEEp vent DNA polymerase. WE have not been able to get amplification with this enzyme. thankyoiu in advance. Jim jurgenson University of Northern Iowa, Jurgenson@cobra.uni.edu From owner-rapd@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: G-418 selection Message-ID: <5A485540669@uamercury.uark.edu> Date: 23 Sep 93 20:04:07 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: University of Arkansas Lines: 28 >Date: Thu, 23 Sep 93 12:52:11 CDT >From: bromberg@ct.med.ge.com (Neil Bromberg 5-5785) >To: yeast@net.bio.net >Subject: G-418 selection >I am trying to find out how to use G-418 selection with electroporation for >yeast transformation. Are cells selected directly on G-418 plates or is it >added after a period of growth. How many hours after plating? I have tried >3 hours and 18 hours without much success. Any suggestions will be greatly >appreciated. > >Please reply to: Susan Bromberg >Susan Bromberg 1833 N. HiMount Blvd >bromberg@ct.med.ge.com Milwaukee WI 53208 One word of caution on something that may be compromising your experiment. Batches of G418 have different specific activities in addition to losing their potency with time. Therefore, you may need to determine the minimum effective concentration. If you are a log higher then you may never get g418 resistance. In a previous life I used G418 on mammalian cells and 24 hours recovery was enough time for them. I can't believe yeast would need more than 10-12 hours. Doug Rhoads || Dept. of Biological Sciences drhoads@mercury.uark.edu || 601 Science Engineering drhoads@uafsysb.uark.edu || University of Arkansas 501-575-3251 || Fayetteville, AR 72701 From owner-rapd@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!TRILLIUM.BOTANY.UTEXAS.EDU!brook From: brook@TRILLIUM.BOTANY.UTEXAS.EDU (Brook Milligan) Newsgroups: bionet.molbio.rapd Subject: analysis of RAPD data Message-ID: <9309231344.AA06956@trillium.botany.utexas.edu> Date: 23 Sep 93 13:44:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 There has been considerable interest on this group over the last few months in various ways of analyzing RAPD data in order to extract genetic information about populations. As some of you know, Mike Lynch and I have completed an analysis of that problem in an effort to correct for the bias necessarily introduced by the dominance. It is now in press in Molecular Ecology, but I am making a postscript version of the manuscript available via anonymous ftp for those of you who wish to make more immediate use of the information. The final version corrects a couple of mistakes present in earlier versions that have been circulated. For those familiar with anonymous ftp the manuscript may be retrieved from pub/RAPDs.ps on trillium.botany.utexas.edu. It is a postscript version including the figures that can be printed on any postscript printer (e.g., Apple Laserwriter). For those of you not familiar with anonymous ftp, check with your local computation center; they will be able to instruct you on how to retrieve documents like this. Finally, I would appreciate it if you notify me when you retrieve the document and if you found any problems with printing it. I am interested in keeping track of the response to this. Thanks, and enjoy your RAPD analyses. Brook G. Milligan Internet: brook@trillium.botany.utexas.edu Department of Botany UUCP: ...!ut-emx!brook University of Texas at Austin (512) 471-3530 Austin, Texas 78713 U.S.A. FAX: (512) 471-3878 From owner-rapd@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!europa.eng.gtefsd.com!uunet!munnari.oz.au!newsroom.utas.edu.au!medicalsc49h103.med.utas.edu.au!user From: Kath.Nesbitt@plant.utas.edu.au Newsgroups: bionet.molbio.rapd Subject: REplies to RAPD analysis Message-ID: Date: 23 Sep 93 05:05:57 GMT Followup-To: bionet.molbio.rapd Organization: University of Tasmania Lines: 61 NNTP-Posting-Host: medicalsc49h103.med.utas.edu.au This is a summary of all the replies I had regarding my query on a programme that would calculate genetic distance an accept missing data for some samples, I hope it helps people Katherine Nesbitt Do you have access to Bionet.software? That might also be a good place to try your luck. Dear Colleague, I have just read yur query about a computer programme which would accept missing data and nevertheless compute genetic distances. Well, I commonly have missing data, and I am happy using BIOSYS programme which can produce different genetic distances, (Nei's, Rogers', etc...). BIOSYS is available from David L. Swofford, Center for Biodiversity, Illinois Natural History Survey 607 E. Peabody Dr. Champaign, Illinois 61820 U.S.A. good luck! GabrielThis may be a case of the blind leading the blind! I am a molecular biologist too, and I know precious little population genetics. PHYLIP is available free by anonymous FTP. Send a message to Felsenstein and he will send back instructions on how to get it. It comes with a lot of documentation which you will have to read in order to answer your question. It is my understanding that PHYLIP includes both phylogenetic and cladistic programs. I have used only a couple of them myself, and I have been interested in population differences rather than phylogeny. There is also a program called PAUP which runs on the Macintosh (promised for DOS soon). I am told it is very slick but I haven't used it yet. It does do phylogeny. It was written by Dave Swofford and costs $100. Technical information is available from paup@onyx.si.edu and PAUP can be ordered from Mary Lou Williamson Center for Biodiversity Illinois Natural History Survey 607 E. Peabody DriveDid you see a recent paper by A.G. Clark and C.M.S. Lanigan in Molecular Biolog y and Evolution vol 10(5):1096-1111. They also provide a computer program for estimating distances using RAPD data. Sudhir KumarI suppose PAUP or NTSYS might do the job. Anyway, could you please post the replies on the RAPD newsgroups, or atleast e-mail me your summary of replies? Thanks. C. S. prakash Tuskegee University Prakash@acd.tusk.eduDear Dr. Nesbitt, There is a Mac version of "mapmaker" available. You can get the program & more information from Pablo Scolnik, I believe. <> Yours sincerely, Alan Slusarenko From owner-rapd@net.bio.net Fri Sep 24 23:00:00 1993 Path: biosci!uwm.edu!psuvax1!psuvm!imeg From: IMEG@psuvm.psu.edu Newsgroups: bionet.molbio.rapd Subject: Statistical analysis using RAPD data Message-ID: <93268.122548IMEG@psuvm.psu.edu> Date: 25 Sep 93 16:25:48 GMT Organization: Penn State University Lines: 6 For your information: Recently Clark and Lanigan (1993) published a paper that provides statistical methods for computing distances and other statistics from RAPD dat a. Clark and Lanigan (1993) Molecular Bioogy and Evolution 10(5):1096-1111. From owner-rapd@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!MUSKWA.UCS.UALBERTA.CA!dchong From: dchong@MUSKWA.UCS.UALBERTA.CA (Chong Daniel) Newsgroups: bionet.molbio.rapd Subject: (none) Message-ID: <9309272147.AA02025@muskwa.ucs.ualberta.ca> Date: 27 Sep 93 21:47:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Subject: Nucleotide divergence in woody plant species We are studing trembling aspen (Populus tremuloides Michx.) populations using RAPD analysis. We used the method of Clark and Lanigan (1993) to estimate nucleotide divergences with some modifications. The nucleotide divergence values detected was 0.05% in average over five populations, which means that 1 in 2000 base pairs is different between aspen populations. Is this figure high for intraspecies level? We could not find any refences from woody species to compare our results. Can someone help us provide some info- mation on this topic? Thank you. Daniel Chong Department of Forest Science University of Alberta From owner-rapd@net.bio.net Tue Sep 28 23:00:00 1993 Path: biosci!ZEKE.PNFI.FORESTRY.CA!LDEVERNO From: LDEVERNO@ZEKE.PNFI.FORESTRY.CA Newsgroups: bionet.molbio.rapd Subject: population analysis Message-ID: <930929112423.4fb2@ZEKE.PNFI.FORESTRY.CA> Date: 29 Sep 93 15:24:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 It seems that there is a number of investigators interested in using rapds to study populations. There seem to be a number of different programs available to perform statistical analysis of rapd data. At this point it may be beneficial if the experts in this type of analysis held some sort of workshop that would address the various aspects of analyzing rapd data from populations, assuming that there is sufficient interest. Any comments? Linda DeVerno From owner-rapd@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Third source for primers? Message-ID: <28dhah$scl@overload.lbl.gov> Date: 30 Sep 93 02:46:41 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 16 NNTP-Posting-Host: s27w007.pswfs.gov I am told that a company, perhaps called "National Biosciences," offers primer kits. I will be happy to summarize any information that I might receive about this company. My interest, as before, is to obtain a name-to-sequence mapping for publicly available primer kits. Thanks, --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!tcsi.tcs.com!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Re: Third source for primers? Message-ID: <28fkpo$fec@overload.lbl.gov> Date: 30 Sep 93 21:58:16 GMT References: <28dhah$scl@overload.lbl.gov> Organization: Dendrome, A Genome Database for Forest Trees Lines: 23 NNTP-Posting-Host: s27w007.pswfs.gov I wrote: >I am told that a company, perhaps called "National Biosciences," >offers primer kits. I will be happy to summarize any information >that I might receive about this company. My interest, as before, >is to obtain a name-to-sequence mapping for publicly available >primer kits. National Bioscience does exist and is in Minnesota. I called them and it seems that they do not sell preset kits of 10-mers, but rather a range of "universal oligonucleotide products." It sounded like they might be willing to whip up a batch to spec, but that was not my interest. [Under no circumstances should this message be construed as endorsement or criticism.] --bks -- Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-rapd@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!PHIBRED.COM!murrayian From: murrayian@PHIBRED.COM (IAN TERSE MURRAY) Newsgroups: bionet.molbio.rapd Subject: Cellulose digestion? Message-ID: <9309301254.AA10587@phibred.phibred.com> Date: 30 Sep 93 12:54:28 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Hello, I was wondering if anyone could tell me of a way to chemically, or otherwise, digest cellulose. I wanted to find a way to destroy the cell wall (without grinding or sonication) so that cell lysis and DNA extraction could be performed. This is a project that I am working on for a University report for my work term. Any references would be appreciated. Murrayian@phibred.com or Rtgrondin@chemistry.watstar.uwaterloo.ca From owner-rapd@net.bio.net Thu Sep 30 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!olivea!charnel!rat!decwrl!usenet.coe.montana.edu!netnews.nwnet.net!ns1.nodak.edu!plains!mcclean From: mcclean@plains.NoDak.edu (Phillip McClean) Newsgroups: bionet.molbio.rapd Subject: Heterozygotes, RIs and Mapping Message-ID: Date: 1 Oct 93 17:42:31 GMT Sender: usenet@ns1.nodak.edu (Usenet login) Organization: North Dakota Higher Education Computing Network Lines: 14 Nntp-Posting-Host: plains.nodak.edu X-Newsreader: TIN [version 1.2 PL1] This might be a multifaceted question, but I will post it anyway. If you are scoring a dominant makers (i.e. RAPDS, disease resistance loci) in a recombinant inbred population with a known percentage of heterozygote lines, what are the consequences of classifying a heterozygote line as a homozygous line? If you are mapping two dominant genes in the same population, what is the effect of misclassification on the linkage distance between any two loci? This are questions that I have considered with regards to an experiment my students are performing and I am not sure what the answer is. Does any one have any thoughts or better yet has anyone solved this problem. Phil McClean mcclen@plains.nodak.edu