From owner-rapd@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!BRADLEY.BRADLEY.EDU!rrs From: rrs@BRADLEY.BRADLEY.EDU (Robert Stephens) Newsgroups: bionet.molbio.rapd Subject: Tom Grothues address Date: 2 Jun 1994 08:56:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Does anyone know Thomas M. Grothues' e-mail address? Last I heard he was at Cal. Sate at ? in greater Los Angeles area. I've already tried the Gopher phone book. Thanks. rrs@bradley.bradley.edu Robert Rhea Stephens Biology Department Bradley University Peoria, IL 61625 From owner-rapd@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!PHIBRED.COM!murrayian From: murrayian@PHIBRED.COM (IAN MURRAY) Newsgroups: bionet.molbio.rapd Subject: Gene tagging using PCR? Date: 2 Jun 1994 06:09:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406021313.AA13363@gw1.phibred.com> NNTP-Posting-Host: net.bio.net Hello, I was wondering if anyone has used primers corresponding to the recognition sites in DNA- ribosomal recognition, TATA or CAAT boxes or transcription factor sequences? Could genes be "tagged" in another way, if you do not have any sequence info on the gene? Thanks. Ian Murray Murrayian@phibred.com From owner-rapd@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!UNAMVM1.DGSCA.UNAM.MX!carvalho From: carvalho@UNAMVM1.DGSCA.UNAM.MX (Carvalho Torres Alexandro cassio-UACPYP) Newsgroups: bionet.molbio.rapd Subject: Re: Conversion of RAPD primers to co-dominant markers? Date: 2 Jun 1994 07:52:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199406011836.OAA06769@postoffice.mail.cornell.edu> NNTP-Posting-Host: net.bio.net On 1 Jun 1994, Muhammad A. Lodhi wrote: > In response to Ian, > There are several articles on cleaved amplified polymorphic sequences > (CAPS), amplification fragment length polymorphisms (AFLPs), sequence > characterized amplified regions (SCARs) and may be some others that could > be used in converting RAPD markers to co-dominant markers. If you need > references about any of these, please let me know. > Muhammad A. Lodhi > Cornell University > ============================================================================= > >Hello again, > > > >Does anyone know how to or has information concerning converting > >RAPD markers to co-dominant markers? > > > >Thanks for you help in advance. > > > >Murrayian@phibred.com > > > >Ian Murray > > > Dear Dr. Lodhi, I would like very much in receiving a reference of some this articles. Thanks a lot. Alexandro Cassio Torres de carvalho Deapartamento de Infectologia, Instituto Nacional de la Nutricion Salvador Zubiran. Mexico, DF From owner-rapd@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!OPUS.MCO.EDU!LEHMANN From: LEHMANN@OPUS.MCO.EDU ("Paul F. Lehmann") Newsgroups: bionet.molbio.rapd Subject: Re: rapd problems Date: 2 Jun 1994 14:32:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HD2PCAHN1E000MHO@opus.mco.edu> NNTP-Posting-Host: net.bio.net Remember to check the oil overlay is not inhibiting the reaction. This was pointed out by others on this list some months ago and was to our great benefit. We switched to the Perkin Elmer super expensive overlay oil after weeks of lousy results with yeast DNAs and hey presto! out popped beautiful patterns. Paul Lehmann, Ph.D. Department of Microbiology, Medical College of Ohio Lehmann%opus@mcoiarc.bitnet From owner-rapd@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!PUCCINI.CRL.UMN.EDU!martinez From: martinez@PUCCINI.CRL.UMN.EDU ("J. Pat Martinez") Newsgroups: bionet.molbio.rapd Subject: Re: Conversion of RAPD primers to co-dominant markers? Date: 3 Jun 1994 07:55:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406031456.JAA01255@puccini.crl.umn.edu> Reply-To: "J. Pat Martinez" NNTP-Posting-Host: net.bio.net In message <9406011358.AA25934@gw1.phibred.com> IAN MURRAY writes: > Hello again, > > Does anyone know how to or has information concerning converting > RAPD markers to co-dominant markers? Yes I vaguely know of two examples, but I haven't used either one. The first method uses the technique Single Standed Conformation Polymorphism (SSCP). Dr. John Taylor of Berkley has used this technique for analyzing fungi with RAPDs. He selects bands that are common to all the isolates (ie they are monomorphic) on traditional agarose gels . He then cuts out these bands, reamplifies them i think. He then uses SSCP techniques to resolve these monomorphic bands further. The patterns are often codominant. The other technique uses Temperature Sweep PAGE. Dr. Mark Penner of Manitoba Canada has used this technique in wheat. I'm not sure exactly how the technique works, but it involves taking bands that are monomorphic by traditional agarose electrophoresis and resolving them on PAGE using Temperature Sweep. I believe many of the RAPD polymorphisms analyzed in this way are also codominant. As far as I know, neither tecnique has been published yet, but I'm trying to get some more information. If I do get some more details, I'll try to send an update. Pat M. % J. Pat Martinez % martinez@puccini.CRL.umn.edu % Dept. of Plant Pathology % Phone (612) 625-2221 % Univ. of Minnesota % Fax (612) 625-9728 From owner-rapd@net.bio.net Mon Jun 06 23:00:00 1994 Newsgroups: bionet.molbio.plant,bionet.molbio.rapd,bionet.plants,bionet.biology.grasses Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!uunet!newsflash.concordia.ca!sifon!VM1.MCGILL.CA From: TINKER Subject: Field sampling of maize tissue for DNA Message-ID: <07JUN94.09999860.0080@VM1.MCGILL.CA> Lines: 10 Sender: usenet@MUSICA.MCGILL.CA Organization: McGill University Date: Tue, 7 Jun 1994 14:15:32 GMT Xref: biosci bionet.molbio.rapd:614 bionet.plants:3343 bionet.biology.grasses:17 I would appreciate hearing from anyone with experience or ideas on sampling plant (especially maize) tissue in the field for future DNA extraction. Thanks, Nick Tinker tinker@agradm.lan.mcgill.ca From owner-rapd@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!CU-DIALUP-0105.CIT.CORNELL.EDU!bl14 From: bl14@cornell.edu (Barbara E. Liedl) Newsgroups: bionet.molbio.rapd Subject: Post-doc position: Plant Genetics/Statistics (2nd posting) Date: Mon, 6 Jun 1994 20:56:54 Organization: Cornell University Lines: 47 Sender: bl14@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0105.cit.cornell.edu POSTDOCTORAL POSITION: PLANT GENETICS A post-doctoral position is available immediately at CORNELL UNIVERSITY, Ithaca, NY. This project is to illucidate the molecular genetic control of the biosynthetic pathway for acylsugars, a class of compounds mediating multiple pest resistance in the wild tomato L. pennellii. The research is directed at determining the role of the genes in identified genomic regions on the biosynthesis of acylsugars and using this information in the transfer of acylsugar-mediated multiple pest resistance to cultivated tomato. The research involves all or part of the following: *Use of an existing map and additional populations to determine the role of each of identified regions in acylsugar biosynthesis *Testing to determine whether any additional regions not yet identified affect types or levels of acylsugars produced *Use of lines segregating for only one of the acylsugar-related genomic regions to improve fine mapping of these regions as a precursor to mapped based cloning. The position is funded by a UDSA/NRI genome grant for up to two years, although application for renewal is expected. QUALIFICATIONS: Applicants MUST have a Ph.D. degree by the time of appointment, along with experience in molecular genetics and plant molecular biological techniques and/or biochemistry (DNA extraction, RFLP techniques, PCR methodology, etc.) and training and/or experience in either statistics or quantitative genetics. An interest in plant improvement is also highly desirable. Experience with QTL mapping is not required. APPLICATION: Send curriculum vitae, brief statement of research accomplishments and goals (less than one page), and list of three references (with phone and FAX numbers) to Dr. Martha A. Mutschler Cornell University Dept. of Plant Breeding and Biometry 303 Bradfield Hall Ithaca, NY 14853 tel: 607-255-1660 fax: 607-255-6683 Email: mam13@cornell.edu From owner-rapd@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!cbr.for.csiro.au!charlie.bell From: charlie.bell@cbr.for.csiro.au (charlie.bell) Newsgroups: bionet.molbio.rapd Subject: Re: Nature of RAPD bands? Date: 9 Jun 1994 16:12:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406092312.AA15305@radiata.cbr.for.CSIRO.AU> NNTP-Posting-Host: net.bio.net >Dear Fellows: >Has anyone tried to work out the nature of RAPD markers in terms of >amplification sites? I am familiar that there are a few reports that >indicate repetitive or single copy nature of RAPDs. What I am interested >in is, if anyone tried to see whether different RAPD bands amplified with >one primer are the result of amplification of a single site with several >internal sites or different sites. Any hint or reference will be >appreciated. I did some work on it and would like to discuss it with >anyone interested. Thanks in advance for your help. > >Muhammad A. Lodhi >New York State Agri. Exp. Station >Cornell University > > Our lab is producing a marker map of Pinus radiata and including RAPD markers. At this time we have about a dozen cases of a single primer givinng two or three loci but there seems to be no pattern yet. Approximately one third of our single primer "pairs" map at the same point (although this may still be many thousand bases away) while the other two thirds seem to have "pairs" with a pretty much random distribution on the same or different chromosomes. It will be some time before our data is published, but other marker maps including RAPDs may already have been published. From owner-rapd@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!CORNELL.EDU!MAL5 From: MAL5@CORNELL.EDU (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: Nature of RAPD bands? Date: 9 Jun 1994 14:12:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406092113.RAA22149@postoffice.mail.cornell.edu> NNTP-Posting-Host: net.bio.net Dear Fellows: Has anyone tried to work out the nature of RAPD markers in terms of amplification sites? I am familiar that there are a few reports that indicate repetitive or single copy nature of RAPDs. What I am interested in is, if anyone tried to see whether different RAPD bands amplified with one primer are the result of amplification of a single site with several internal sites or different sites. Any hint or reference will be appreciated. I did some work on it and would like to discuss it with anyone interested. Thanks in advance for your help. Muhammad A. Lodhi New York State Agri. Exp. Station Cornell University From owner-rapd@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!barrnet.net!biosys!apldbio.com From: dak@apldbio.com (Dave Knorr) Newsgroups: bionet.molbio.plant,bionet.molbio.rapd,bionet.plants,bionet.biology.grasses Subject: Re: Field sampling of maize tissue for DNA Message-ID: <1114@biosys.apldbio.COM> Date: 10 Jun 94 18:49:38 GMT References: <07JUN94.09999860.0080@VM1.MCGILL.CA> Sender: news@biosys.apldbio.COM Followup-To: bionet.molbio.plant Organization: Perkin Elmer/Applied Biosystems Lines: 18 X-UserAgent: Nuntius v1.1.1d24 X-XXDate: Fri, 10 Jun 94 19:49:21 GMT Xref: biosci bionet.molbio.rapd:618 bionet.plants:3379 bionet.biology.grasses:20 In article <07JUN94.09999860.0080@VM1.MCGILL.CA> TINKER, CZNT000@MUSICA.MCGILL.CA writes: In article <07JUN94.09999860.0080@VM1.MCGILL.CA> TINKER, CZNT000@MUSICA.MCGILL.CA writes: >I would appreciate hearing from anyone with experience or ideas >on sampling plant (especially maize) tissue in the field for >future DNA extraction. > >Thanks, >Nick Tinker >tinker@agradm.lan.mcgill.ca I am also interested in how people do this. Particularly if there is any convenient way to begin the extraction process and hold the samples (say 24-48 hours) without refrigeration. Dave Knorr dak@apldbio.com From owner-rapd@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Nature of RAPD bands? Date: 10 Jun 1994 07:37:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406101432.AA09983@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net In respones to Muhammad Lodhi's question about the nature of RAPD bands: Most of the RAPD bands generated with a given RAPD primer come from different genetic loci. However, occasionally one sees co-dominant RAPD polymorphisms, that is RAPD bands that differ in size between individuals, but come from the same locus. A single individual , if heterozygous for such RAPd locus, may therefore have two bands comina from the same locus. SOmetimes one also sees in RAPD paatterns single strands, or other aberrant amplification products that appear to be related (as shown by SAouthern hybridization). Some of this was discussed in the Methods in Enzymology article (Williams et al.). Antoni Rafalski From owner-rapd@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!CORNELL.EDU!MAL5 From: MAL5@CORNELL.EDU (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: Re: Nature of RAPD bands? Date: 10 Jun 1994 11:54:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406101854.OAA26487@postoffice.mail.cornell.edu> NNTP-Posting-Host: net.bio.net >From: rafalski@esvax.dnet.dupont.com >Date: Fri, 10 Jun 1994 12:40:04 -0400 >To: mal5@cornell.edu (Muhammad Atif Lodhi) >Apparently-To: mal5@cornell.edu >Subject: Re: Nature of RAPD bands? > >Muhammad, >I remember a paper from Tom Shenk's lab a couple of years ago, in which he >used a single primer specific to some gene he was interested in, in RAPD >conditions. He got many bands and characterized some of them by >sequencing. Most of the bands started with that specific sequence that >corresponded to his primer, and extended various distances outward. This >supports your idea (and the observations of the CSIRO pine guys) that some >of the bands are related. This would happen especially if the primer was >exactly matched to one site in the genome, as in Shenk et al. > >I am sending this just to you, so you may want to re-post it to the RAPD >bulletin, if others may be interested. > >Antoni > > From owner-rapd@net.bio.net Fri Jun 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!yale.edu!noc.near.net!saturn.caps.maine.edu!maine.maine.edu!aparker Organization: University of Maine System Date: Sat, 11 Jun 1994 13:40:07 EDT From: Message-ID: <94162.134007APARKER@MAINE.MAINE.EDU> Newsgroups: bionet.molbio.rapd Subject: M13 RAPDs Lines: 15 It has recently come to my attention that several labs are having good luck using the unversal plasmid/M13 sequencing primers (the 17mers, I imagine) as RAPD (or AP-PCR, for the squeamish) primers. The work I've heard of has been done on fishes, but it may be that these primers are being used on other groups as well. If anyone is experienced in doing this, I'd very mech like to see your protocols (eg amount of DNA, [primer], [Mg++], cycling parameters, etc). Thanks in advance, Alex Parker aparker@maine.maine.edu From owner-rapd@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!qmrelay.mail.cornell.edu!warren_lamboy From: warren_lamboy@qmrelay.mail.cornell.edu ("Warren Lamboy") Newsgroups: bionet.molbio.rapd Subject: Question about RAPD bands Date: 13 Jun 1994 06:00:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <94Jun13.090134edt.577501-5@cornell.edu> NNTP-Posting-Host: net.bio.net Subject: Time:8:29 OFFICE MEMO Question about RAPD bands Date:13/06/1994 To the RAPD netters: We have just begun doing RAPDs in our lab, and I have a question or two that I hope someone can shed some light on, or at least share their opinions about. In our lab, after freeze-drying a sample of plant material (very young cabbage leaves), the material is divided into two subsamples. One worker extracts DNA, dilutes it to the proper concentration, sets up and carries out PCR (with a single primer) and runs gels on the first sample. The second worker carries out the whole procedure on the second sample. The first worker inevitable finds many more amplified fragments than the second worker. All of the bands that show up strongly under UV after staining with Ethidium bromide are the same for both workers. The additional bands that worker one finds are "faint." My questions are: 1. Has anyone seen data on or does anyone have data that bears on the question of whether the "faint" bands are real? That is, do they possess sequence complementary to the primer sequence? Can we assume that they do not real (as defined above)? 2. If the faint bands are usually not real, what are they? Do they indicate damaged DNA? Do they indicate inadequate removal of protein, carbohydrates, etc.? Damaged primers? Or is the absence of the faint bands in sample two the problem? Any ideas, data, or opinions anyone has concerning this issue would be greatly appreciated. - Warren_Lamboy@cornell.edu From owner-rapd@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!BCRSSU.AGR.CA!WILLIS From: WILLIS@BCRSSU.AGR.CA Newsgroups: bionet.molbio.rapd Subject: DNA extraction protocol for moths needed Date: 13 Jun 1994 09:40:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HDHSGIPI4Y00175V@GW.AGR.CA> NNTP-Posting-Host: net.bio.net Hello: I am interested in obtaining a quick and easy protocol for the extraction of DNA from adult leaf rollers. I plan to screen several species of leaf rollers with RAPD primers. In the past I have used a KAc/isopropanol method (originally developed for Drosophila). I'm concerned that the wings etc. of the moth may be a problem during extraction. If anyone has a method they would like to share with me I would appreciate it. You can Email me directly at Willis@BCRSSU.AGR.CA. Thanks in advance. Les. -----------------------------------------(=)----------------------------------- | Les Willis / | | Agriculture Canada Research Station (=) | | Summerland, British Columbia / | | Canada (=) | | V0H 1Z0 / | | Email Address: WILLIS@BCRSSU.AGR.CA (=) | ------------------------------------------/------------------------------------ From owner-rapd@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!dsammata From: dsammata@magnus.acs.ohio-state.edu (Diana Sammataro) Newsgroups: bionet.molbio.rapd Subject: reusing agarose gels Date: 13 Jun 1994 11:27:14 GMT Organization: The Ohio State University Hello everyone. I am back doing RAPDs and have heard of reusing agarose gels from someone on the net a while back. Is this possible? How does one go about doing it? How many times can one reuse the gels? What happens to the DNA and EB? Lines: 6 Distribution: usa Message-ID: <2thfqi$5od@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu And can EB be reused? If you evaporate it can the crystals be re- claimed and if not, how do you dispose them? Thanks in advance. Diana From owner-rapd@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!SGGW.SGGW.WAW.PL!wochniak From: wochniak@SGGW.SGGW.WAW.PL Newsgroups: bionet.molbio.rapd Subject: Thermal Cycler Date: 14 Jun 1994 07:33:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <94061416345932@sggw.sggw.waw.pl> NNTP-Posting-Host: net.bio.net Hi netters, which cycler did you find the most reliable and not to expensive to bye? Which one will be the best choise for RAPD work and will allow analyse as many samples as possible? Which has good parameters and which parameters are of interest? Thanks for your time for giving advice for young scientists. Please contact me: wochniak@sggw.sggw.waw.pl. Peter. From owner-rapd@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!GPU.SRV.UALBERTA.CA!dchong From: dchong@GPU.SRV.UALBERTA.CA (Daniel Chong) Newsgroups: bionet.molbio.rapd Subject: Reference Date: 15 Jun 1994 16:07:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters; I urgently need some info on the two following references and your help will be greatly appreciated. Aquadro CF (1992) Molecular population genetics of Drosophila. In: Molecular approach to pure and applied entomology,pp 222-266, Springer Verlag. I have the paper but not the book. Can anyone out there tell me the names of the editor(s) ? Lynch M, Milligan BG (1993) Analysis of population genetic structure with RAPD markers. Molecular Ecology. Again, I have the manuscript and need to know the volume and page number. I think the paper has been published. Our library does not have both items and I need this info for the proof of my paper. Thank you. Daniel Chong University of Alberta From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!AGRADM.Lan.McGill.CA!TINKER From: TINKER@AGRADM.Lan.McGill.CA ("Nick Tinker") Newsgroups: bionet.molbio.rapd Subject: RAPD homology to other fragments Date: 16 Jun 1994 06:51:08 -0700 Organization: McGill University, Macdonald Campus Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406161351.JAA26115@sifon.CC.McGill.CA> NNTP-Posting-Host: net.bio.net I have some additional experience that I would like to add to the Muhammad Lodhi's post about homology among RAPD bands. In our work on RAPDs in barley (Tinker, Mather & Fortin, TAG 85:976-984) we wanted to see whether polymorphic bands were homologous to other reaction products, so we probed Southerns of the reactions with the target fragment. We tried about eight of these, and the polymorphic band seemed to have a unique sequence among the reaction products. Something I might add is that all of these were clear, strong polymorphisms, and we washed quite stringently, so it is possible that there was homology to VERY weak bands that we couldn't see. In several cases there WAS a faint homologous band just below the target band but it was also polymorphic, and it had the same segregation pattern as the target fragment. My hypothesis is that these are "sub- amplification products" from within the main fragment. Has anyone else observed these? The above work led to our hypothesis that it might sometimes be useful to score RAPD markers without running them on a gel; ie, by spotting reaction products on a membrane and probing them with the target fragment. This too has worked for strong RAPD markers, and some results are shown in a note by Aitken, Tinker, Mather & Fortin, Genome 37:506-508. =========================================================== Nick Tinker EMAIL: tinker@agradm.lan.mcgill.ca Plant Science Dept. PHONE: 514-398-8733 McGill University FAX: 514-398-7897 =========================================================== From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!CORNELL.EDU!MAL5 From: MAL5@CORNELL.EDU (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: Summary: Nature of RAPD bands? Date: 16 Jun 1994 04:00:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 117 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406161101.HAA19295@postoffice.mail.cornell.edu> NNTP-Posting-Host: net.bio.net Here is the summary of the messages that I got in response to "Nature of RAPD bands?". Posting it with the intention that it might be of interest to others too. Muhammad "Dear Fellows: Has anyone tried to work out the nature of RAPD markers in terms of amplification sites? I am familiar that there are a few reports that indicate repetitive or single copy nature of RAPDs. What I am interested in is, if anyone tried to see whether different RAPD bands amplified with one primer are the result of amplification of a single site with several internal sites or different sites. Any hint or reference will be appreciated. I did some work on it and would like to discuss it with anyone interested. Thanks in advance for your help". Muhammad A. Lodhi New York State Agri. Exp. Station Cornell University ================================================================================ Hi! I've been doing RAPDs on Mycobacterium avium for the past year or so. One epxeriment which I did recently was to arbitrarily pick one band from a RAPD profile generated from a single primer, extract it from the gel, make a probe via random priming, and probe the rest of the bands from that profile. The results I got were very interesting. For each of three primers, the probe bound to more than one band, suggesting that there is some overlap in bands generated from a single primer. However, not all of the bands from a profile hybridized to the probe. This suggests to me that at least some of the bands are homologous. My original thought was that this resulted from several primer binding sites within a stretch of DNA allowing amplification of different sized bands. This is still my primary hypothesis. At a meeting I attended recently, someone also suggested that since a lot of IS elements have been found in M. avium, the homology between different bands could be the result of amplifica tion of repetitive DNA which could be located anywhere in the genome. This is what I've observed with my RAPDs. I'm interested to know if others have gotten the same results. Sincerely, Donna M. Jensen JOFTOPSM@VTVM1.cc.vt.edu ................................................................................ Muhammad, I remember a paper from Tom Shenk's lab a couple of years ago, in which he used a single primer specific to some gene he was interested in, in RAPD conditions. He got many bands and characterized some of them by sequencing. Most of the bands started with that specific sequence that corresponded to his primer, and extended various distances outward. This supports your idea (and the observations of the CSIRO pine guys) that some of the bands are related. This would happen especially if the primer was exactly matched to one site in the genome, as in Shenk et al. I am sending this just to you, so you may want to re-post it to the RAPD bulletin, if others may be interested. Antoni ................................................................................ I have done some probing of multiple RAPD bands with a probe based on one of them (getting ready to submit ms). The results were quite varied. Clearly not all bands are variants of one sequence but many have substantial sequence similarity. What is leading you to this question? I would be interested in hearing of your experience. Laura Adamkewicz (ladamkew@mason1.edu) Dept. of Biology George Mason University Fairfax, VA 22030 (703) 993-1047 ................................................................................ charlie.bell@cbr.for.csiro.au (Charlie Bell) wrote, Our lab is producing a marker map of Pinus radiata and including RAPD markers. At this time we have about a dozen cases of a single primer giving two to three loci but there seems to be no pattern yet. Approximately one third of our single primer "pairs" map at the same point (although this may still be many thousand bases away) while the other two thirds seem to have "pairs" with a pretty much random distribution on the same or different chromosomes. It will be some time before our data is published, but other markers maps including RAPDs may already have been pulblished. ................................................................................ G'Day I did a couple of southern blot hybridization with a rapd band as a probe and found that bandsof one size are identical across trains (streptococci anyway) and don't hybridize to bands of dissimilar size. I'm thinking of sequencing a few of these bands to see if they are similar. Regards Don Gardiner Menzies School of Health Research Darwin Australia ................................................................................ Hi Muhammad, In most every paper I encountered on southern hybridization of RAPD fragments to their "home" pattern, I noticed that more than one, but not every fragment, has similar sequence. I myself did several sothernblots on RAPD patterns of Drosophila. The same result, sometimes only one, but in most cases two bands light up. Stringent washing conditions did not solve the riddle. Seems to me that at least some fragments within a pattern are derived from one and the same locus. It would, however, be an error to think that ALL fragments are. The presence of highly repetitive sequences in RAPD fragments of course prevents any certainty as to their origins. Hope that sounds reasonable enough to you. Good Luck, L.van de Zande Dept. of Genetics University of Groningen P.O.Box 14 9750 AA Haren The Netherlands Tel. +31 50 632126 Fax. +31 50 632348 ...................................END.......................................... From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bham!bhamvx!baranskr From: baranskr@vms1.bham.ac.uk Newsgroups: bionet.molbio.rapd Subject: subscribe Date: 16 Jun 94 14:15:54 GMT Organization: University of Birmingham Lines: 2 Message-ID: <1994Jun16.141554.1@vms1.bham.ac.uk> NNTP-Posting-Host: vms1.bham.ac.uk subscribe RAFAL BARANSKI BARANSKR@BHAM.AC.UK From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Postdoc Opening Date: 16 Jun 1994 08:10:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406161501.AA04020@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net DuPont Molecular Breeding group expects to have an opening for a postdoc or visiting scientist at the beginnig of 1995, to work on the development of molecular marker systems for higher plants, especially microsatellites (simple sequence repeats) and AFLPs, and/or on mapping of traits of agronomic importance. Skills in molecular biology and/or genetics are required. The Principal Investigators in the group include Julie Vogel, Mike Hanafey, Antoni Rafalski and Scott Tingey. Please send applications to Scott Tingey, DuPont Agricultural Biotechnology, PO Box 80402, Wilmington, DE 19880-0402, tel. 302-695-7252, e-mail "tingesv@esvax.dnet.dupont.com". Antoni Rafalski From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Kevin O'Donnell" Newsgroups: bionet.molbio.rapd Subject: identification of transgenics using RAPDs Date: 16 Jun 1994 16:00:02 +0100 Lines: 25 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2tppdi$2tk@mserv1.dl.ac.uk> Reply-To: odonnell@sasa.gov.uk Original-To: rapd@dl.ac.uk We are interested in using RAPDs to identify (potato) plants with inserted gen material. Can anyone tell me if using RAPDs is a good way of doing this? How many primers would we need to try before we had a high (90%) probability of detecting, say a 3Kb insert? What is the lowest level of variation which RAPDs can detect? Apologies if this is a thread which has been followed in the near past - I have only just got access to the biosci newsgroups. Kevin O'Donnell Scottish Agricultural Science Agency "We must combine pessimism East Craigs of the intellect with Edinburgh Tel. 031 244 8924 optimism of the will." EH12 8NJ Fax 031 244 8940 Scotland Antonio Gramsci odonnell@jura.sasa.gov.uk From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!columba.udac.uu.se!populus.slu.se!jokarlsson!jan-olof.karlsson From: jan-olof.karlsson@mykopat.slu.se (Jan-Olof Karlsson) Newsgroups: bionet.molbio.rapd Subject: Re: M13 RAPDs Date: Thu, 16 Jun 1994 16:43:40 Organization: Dept. of Forest Mycology and pathology, Swedish University of Agricultural Scien Lines: 34 Message-ID: References: <94162.134007APARKER@MAINE.MAINE.EDU> NNTP-Posting-Host: jokarlsson.mykopat.slu.se X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <94162.134007APARKER@MAINE.MAINE.EDU> writes: >Date: Sat, 11 Jun 1994 13:40:07 EDT >From: >Subject: M13 RAPDs >It has recently come to my attention that several labs are having >good luck using the unversal plasmid/M13 sequencing primers (the >17mers, I imagine) as RAPD (or AP-PCR, for the squeamish) primers. >The work I've heard of has been done on fishes, but it may be that >these primers are being used on other groups as well. >If anyone is experienced in doing this, I'd very mech like to see >your protocols (eg amount of DNA, [primer], [Mg++], cycling >parameters, etc). >Thanks in advance, >Alex Parker >aparker@maine.maine.edu We have been working some time with M13 core sequence as a primer for PCR-reactions. For a description of methods see Mycological Research vol 98 1994, pages 57-63. Stenlid, Karlsson and Högberg. We have found this primer to be easy to work with, giving consistent results. It has often given amplification when other (shorter) RAPD-primers have not . The primer sequence is GAGGGTGGCGGTTCT. If you have any questions send me a mail. Jan-Olof.Karlsson@mykopat.slu.se From owner-rapd@net.bio.net Wed Jun 15 23:00:00 1994 Path: biosci!esvax.dnet.dupont.com!rafalski From: rafalski@esvax.dnet.dupont.com Newsgroups: bionet.molbio.rapd Subject: Probing RAPD dot blots Date: 16 Jun 1994 07:58:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406161451.AA03699@esds01.es.dupont.com> NNTP-Posting-Host: net.bio.net We investigated quite thoroughly the concept discussed in the message from Nick Tinker: to probe RAPD dot blots with isolated RAPD band probes, instead of running RAPDs on gels. We used Biomek robot to spot about 1000 or so small dots on a nylon membrane mounted in a frame. The membrane was then denatured in NaOH, and the pattern of dots was probed with isolated RAPD band probes. Chemiluminescent probes were used, and the whole membrane was imaged by a CCD camera for automated scoring. The results are good, as long as your probe is clean. In many cases we found it necessary to clone the RAPD band to obtain clean segregation pattern. (Work by Phyllis Biddle, Mike Hanafey, Pete Kieselbach and others in DuPont AgBiotech) A further extension of this concept is a microtiter dish DNA capture assay that we also developed (a manuscript is ready and hopefully I will find some time soon to finish the editing and publish it). Antoni Rafalski From owner-rapd@net.bio.net Thu Jun 16 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Kevin O'Donnell" Newsgroups: bionet.molbio.rapd Subject: Transgenics problem expanded on Date: 17 Jun 1994 11:00:21 +0100 Lines: 31 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2trs7l$kk7@mserv1.dl.ac.uk> Reply-To: odonnell@sasa.gov.uk Original-To: rapd@dl.ac.uk Perhaps it would be helpful if I enlarge upon my problem re detecting transgenic potato plants. The problem is this:if I am given a potato of unknown origin, is there any way that I can easily test to see if it contains an insert? There should be no problem determining which variety of potato it is as we are constructing a database of RAPD profiles of all varieties. Potatoes are particularily amenable to this approach as they are vegetatively propagated. Having a RAPD database to pick out varieties it would be useful to able to use it to pick out transgenics and also somaclonal variants. From the replies I have received already (thank you) it seems that RAPDs are not really a feasable way of doing this, so it may not be totally appropriate to post in this newsgroup. Perhaps someone knows of a better method for detecting small genomic changes? Kevin O'Donnell Scottish Agricultural Science Agency "We must combine pessimism East Craigs of the intellect with Edinburgh Tel. 031 244 8924 optimism of the will." EH12 8NJ Fax 031 244 8940 Scotland Antonio Gramsci odonnell@jura.sasa.gov.uk From owner-rapd@net.bio.net Thu Jun 16 23:00:00 1994 Path: biosci!SGGW.SGGW.WAW.PL!wochniak From: wochniak@SGGW.SGGW.WAW.PL Newsgroups: bionet.molbio.rapd Subject: Looking for MJ Research address Date: 17 Jun 1994 02:58:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <94061712004127@sggw.sggw.waw.pl> NNTP-Posting-Host: net.bio.net Hi netters, does anyone know any contact via s-mail or e-mail to the MJ Research company? We would like to buy a thermocycler and need a price list. Any suggestion? Peter Please answer: wochniak@sggw.sggw.waw.pl From owner-rapd@net.bio.net Thu Jun 16 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!nctuccca.edu.tw!netnews.ntu.edu.tw!ccms!r2601105 From: r2601105@ccms.ntu.edu.tw (Shyh-Rong Chang) Newsgroups: bionet.molbio.rapd Subject: re: reusing agarose gels Date: 17 Jun 1994 06:17:13 GMT Organization: National Taiwan University Lines: 10 Message-ID: <2trf59$c66@netnews.ntu.edu.tw> NNTP-Posting-Host: r2601105@ccms.ntu.edu.tw X-Newsreader: TIN [version 1.2 PL2] hi diana: I'm undergraduate student of ntu in taiwan (national taiwan university) call me choo. In my experience,EB can reuse but just for few times,then you have to discard it because it dirts your gel. You can get an empty platic can to collect EB solution,and when it's full add active charcoal (or carbon) to absorb EB,then pass this can to the school or someone that collect it. About the amount of active charcoal to add,100mg active charcoal for 100ml EB dilute solution. From owner-rapd@net.bio.net Thu Jun 16 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!eunet.no!nuug!EU.net!uunet!nctuccca.edu.tw!netnews.ntu.edu.tw!ccms!r2601105 From: r2601105@ccms.ntu.edu.tw (Shyh-Rong Chang) Newsgroups: bionet.molbio.rapd Subject: watermelon DNA extraction protocol needed Date: 17 Jun 1994 05:18:04 GMT Organization: National Taiwan University Lines: 8 Message-ID: <2trbmc$b2h@netnews.ntu.edu.tw> NNTP-Posting-Host: r2601105@ccms.ntu.edu.tw X-Newsreader: TIN [version 1.2 PL2] well,I encounter many problems,one of them are,after CTAB extraction and repurify the Genomic DNA by using phenol-chloroform and 24:1 isoamyl alcohol:chloroform and I use absolute EtOH to ppt the Genomic some of them disolve very well,some of them cannot. HELP!!!!! the watermelon leaf that I use was old stock but not long it was leaf powder that never leave -70C for about 2 months,so I need some new protocol about Extraction of Genomic DNA from watermelon. thanks in advance....:) From owner-rapd@net.bio.net Sun Jun 19 23:00:00 1994 Path: biosci!CHRISTA.UNH.EDU!sbenard From: sbenard@CHRISTA.UNH.EDU (Susan A Benard) Newsgroups: bionet.molbio.rapd Subject: RAPD reproducibility Date: 20 Jun 1994 09:43:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Help! Under what we believe are identical reaction conditions with the same template DNA we lack reproducibility from day to day in the quality of our amplifications not in the banding pattern. We use an MJ thermocycler and an oven style thermocycler. We experience the same problem with each. We are using Promega enzyme and buffer although we have tried PE with similar results. Suggestions are appreciated! Susan Adam Benard Dept. of Biochemistry UNH Durham, NH From owner-rapd@net.bio.net Mon Jun 20 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!ghost.dsi.unimi.it!genes!heitor From: heitor@genes.icgeb.trieste.it (Heitor Luiz da C. Coutinho) Subject: Re: RAPD reproducibility Message-ID: <1994Jun21.143239.10808@genes.icgeb.trieste.it> Organization: ICGEB References: Date: Tue, 21 Jun 1994 14:32:39 GMT Lines: 55 sbenard@CHRISTA.UNH.EDU (Susan A Benard) writes: >Help! Under what we believe are identical reaction conditions with >the same template DNA we lack reproducibility from day to day in the >quality of our amplifications not in the banding pattern. We use an >MJ thermocycler and an oven style thermocycler. We experience the >same problem with each. We are using Promega enzyme and buffer although >we have tried PE with similar results. >Suggestions are appreciated! >Susan Adam Benard >Dept. of Biochemistry >UNH >Durham, NH > Hi, Susan, I would try testing different enzymes. Have you done thatt? I had problems with reproducibilty and found that the major factor affecting the poor results was the polymerase, Promega, by the way. Good luck! Heitor L.C. Coutinho Funda@ao Tropical Andre Tosello Campinas, Brazil From owner-rapd@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.rapd Subject: Sorted List of Primers Available Date: 22 Jun 1994 18:21:48 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 47 Distribution: world Message-ID: <2u9vfs$2o5@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov We have added the sequences of 200 primers that are available from Genosys to our collation of RAPD primers. You can retrieve the list of 2000 primers sorted by sequence from out gopher server at s27w007.pswfs.gov port 70. You can also reach the Dendrome gopher from our WWW server at URL http://s27w007.pswfs.gov/ Once you get to the gopher select: --> 6. Forest tree genome resources (including TreeGenes)/ --> 5. Primers/ --> 2. RAPD Primers/ And you will see these files: RAPD Primers --> 1. Duplicate_primers. 2. Genosys_Operon_UBC_sorted. 3. Genosys_primers. 4. Operon_UBC_Overlap. 5. Operon_UBC_alphabetic_by_sequence. 6. Operon_primers. 7. UBC_primers. [Items 4 & 5 are now out of date, but will remain for a while]. We are very interested in keeping this resource up to date. Please let me, or David Harry (deh@s27w007.pswfs.gov), know of any other sources of RAPD primer kits. The Dendrome project intends to be a central electronic resource for the study of the molecular biology of forest trees. We welcome all researchers in this area to the collaboration. Funding for Dendrome and TreeGenes is from the USDA ARS Plant Genome Research Program. --bks -- Bradley K. Sherman Computer Scientist Dendrome Project 510-559-6437 FAX: -6440 Institute of Forest Genetics bks@s27w007.pswfs.gov P.O. Box 245, Berkeley, CA 94701 http://s27w007.pswfs.gov/People/bks.html From owner-rapd@net.bio.net Thu Jun 23 23:00:00 1994 Path: biosci!agate!ames!purdue!mozo.cc.purdue.edu!inet.d48.lilly.com!mcvax2.d48.lilly.com!swift Newsgroups: bionet.molbio.rapd Subject: re:Reference Message-ID: <1994Jun16.124422.1@mcvax2.d48.lilly.com> From: swift@mcvax2.d48.lilly.com Date: 16 Jun 94 12:44:22 EST Distribution: world Nntp-Posting-Host: mcvax2.d48.lilly.com Lines: 5 M. Lynch and B.G. Milligan Molec Ecol v3, p 91-99 1994 From owner-rapd@net.bio.net Fri Jun 24 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.molbio.rapd Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 25 Jun 1994 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 319 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406250900.CAA14913@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. 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For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-rapd@net.bio.net Mon Jun 27 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!ns1.nodak.edu!plains!borovkov From: borovkov@plains.NoDak.edu (Alex Borovkov) Subject: DNA folding Sender: usenet@ns1.nodak.edu (Usenet login) Message-ID: Date: Tue, 28 Jun 1994 15:22:49 GMT Nntp-Posting-Host: plains.nodak.edu Organization: North Dakota Higher Education Computing Network X-Newsreader: TIN [version 1.2 PL2] Lines: 27 [ Article crossposted from bionet.molbio.methds-reagnts,bionet.molbio.genbank ] [ Author was Alex Borovkov ] [ Posted on Fri, 24 Jun 1994 15:20:34 GMT ] Hi Networkers, does anybody know any software for DNA folding. For RNA folding I've been using PCfold and RNAfold, but these softwares don't have a DNA folding option. In order to use them for folding DNA the energy file need to be modified, but I don't know how. Any recommendation on a program with DNA folding option or how to modified the energy file to make it suitable for folding DNA will be greatly appreciated. Sincerely, -- Dr. Alex Borovkov, | Please excuse me for my English. Plant Pathology Dept., | My Russian is getting worse too North Dakota State University | and soon I will know nothing Fargo, ND 58105 | but few dirty words tel: 701 237 8340 ; FAX: 701 237 7851 ; Internet: borovkov@plains.NoDak.edu. -- Dr. Alex Borovkov, | Please excuse me for my English. Plant Pathology Dept., | My Russian is getting worse too North Dakota State University | and soon I will know nothing Fargo, ND 58105 | but few dirty words tel: 701 237 8340 ; FAX: 701 237 7851 ; Internet: borovkov@plains.NoDak.edu. From owner-rapd@net.bio.net Mon Jun 27 23:00:00 1994 Path: biosci!PHIBRED.COM!murrayian From: murrayian@PHIBRED.COM (IAN MURRAY) Newsgroups: bionet.molbio.rapd Subject: Summary of chelex DNA extraction? Date: 28 Jun 1994 11:29:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406281835.AA04751@gw1.phibred.com> NNTP-Posting-Host: net.bio.net From: GW1::"MAILER-DAEMON" "Mail Delivery Subsystem" 28-JUN-1994 13:04:33.09 To: CC: Subj: Returned mail: User unknown ----- Transcript of session follows ----- <<< RCPT To: <<< DATA >>> RCPT To: <<< 550 ... User unknown 550 ... User unknown ----- Unsent message follows ----- Received: from PDS.DECnet MAIL11D_V3 by gw1.phibred.com (5.57/Ultrix3.0-C) id AA01586; Tue, 28 Jun 94 13:08:05 -0500 Date: Tue, 28 Jun 94 13:08:05 -0500 From: pds::murrayian (IAN MURRAY) To: GW1::"rapds@net.bio.net" Subject: Send summary of chelex DNA extraction? I know that there was a discussion concerning chelex extraction a long time ago. I was wondering if anyone could send a summary to the billboard or myself? Murrayian@phibred.com Murrayian@phibred.com Pioneer Hibred Canada From owner-rapd@net.bio.net Mon Jun 27 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!br-ba.plants.umanitoba.ca!blatta From: blatta@bldgagric.lan1.umanitoba.ca (James E. Blatta) Newsgroups: bionet.molbio.rapd Subject: DNA extraction protocol for green foxtail or corn wanted Date: Tue, 28 Jun 1994 18:11:56 GMT Organization: Plant Science Dept. Lines: 3 Message-ID: NNTP-Posting-Host: br-ba.plants.umanitoba.ca X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] DNA extraction protocol for green foxtail (Setaria viridis) is wanted. The DNA will be used for RAPD analysis. A protocol for corn or any other C4 species may also be useful. Please reply by e-mail. From owner-rapd@net.bio.net Tue Jun 28 23:00:00 1994 Newsgroups: bionet.molbio.rapd Path: biosci!agate!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!olivea!decwrl!pa.dec.com!BIX.com!ghurst From: ghurst@BIX.com Subject: Arbitrary primer library Message-ID: <9406291302.memo.98234@BIX.com> Date: Wed, 29 Jun 1994 13:02:02 -0400 (EDT) X-Received: by usenet.pa.dec.com; id AA23783; Wed, 29 Jun 94 10:14:10 -0700 X-Received: by pobox1.pa.dec.com; id AA18705; Wed, 29 Jun 94 10:14:07 -0700 X-Received: from bos2a.delphi.com by inet-gw-2.pa.dec.com (5.65/27May94) id AA26569; Wed, 29 Jun 94 10:09:45 -0700 X-Received: from bix.com by delphi.com (PMDF V4.3-7 #6563) id <01HE462OYIC090TE64@delphi.com>; Wed, 29 Jun 1994 13:07:39 EDT X-Received: by bix.com (CoSy3.31.1.45) id <9406291302.memo.98234@BIX.com>; Wed, 29 Jun 1994 13:02:02 -0400 (EDT) X-To: bionet.molbio.rapd.usenet@decwrl.dec.com X-Content-Transfer-Encoding: 7BIT X-Cosy-To: bionet.molbio.rapd.usenet@decwrl.dec.com Lines: 25 Genosys Biotechnologies Inc. is seeking participants for a collaborative synthesis project. We would like to synthesize 1000 10-mers to create a resource for researchers doing work with arbitrary priming methods. This DecamerArray(TM) would be available at a reasonable price and consist of 0.1 OD of each sequence placed into eleven 96-well plates. Each oligo is desalted. Genosys is interested in finding 9 or more researchers that would be interested in this product. Fewer than nine interested parties could be involved, but this would drive up the price of each copy of the library. As an incentive, if 9 or more researchers agree to participate, we will decrease the cost of the library for the first eight participants by 15%. If there are more than 30 participants, we will decrease the cost to the first eight by 30%. The characteristics of the library are up to the participants to agree on. This project is highly flexible and will respond to the desires of the researchers involved. Delivery could be in a matter of two to three weeks after the contents of the library are decided. If this project is of interest, please contact Gerald D. Hurst, Science Director at (800) 2345-DNA, FAX (713) 363-2212, or email: ghurst@bix.com. Sincerely, Gerald Hurst From owner-rapd@net.bio.net Tue Jun 28 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.oz.au!yoyo.aarnet.edu.au!news.adelaide.edu.au!cford From: cford@waite.adelaide.edu.au (Chris Ford) Newsgroups: bionet.molbio.rapd,bionet.molbio.methds-reagnts Subject: Method for Amplified Fragment Length Polymorphism Analysis Date: 29 Jun 1994 05:41:05 GMT Organization: The University of Adelaide, Waite Campus Lines: 4 Message-ID: <2ur1hh$o42@quandong.itd.adelaide.edu.au> NNTP-Posting-Host: schooner.waite.adelaide.edu.au Summary: Looking for a method/protocol/reference for the AFLP technique Keywords: AFLP Faculty: Agricultural & Natural Resource Sciences Xref: biosci bionet.molbio.rapd:645 bionet.molbio.methds-reagnts:15745 Does anybody know of a published reference for the AFLP technique, or even have a protocol that they're willing to share. Thanks very much, Nick Paltridge. From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!UXA.CSO.UIUC.EDU!jerbear From: jerbear@UXA.CSO.UIUC.EDU ("Jerry Hill") Newsgroups: bionet.molbio.rapd Subject: RE: QTL analysis and variance of categorized data Date: 1 Jul 1994 10:34:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <45334.jerbear@uxa.cso.uiuc.edu> Reply-To: jerbear@uxa.cso.uiuc.edu NNTP-Posting-Host: net.bio.net In Message 1 Jul 1994 08:12:00 -0700, MAL5@cornell.edu (Muhammad A. Lodhi) writes: > >In MAPMAKER/QTL we get variance explained for each QTL peak. My colleague >says that variance can't be calculated in categorized data of a trait. > >My questions are; >Whether he is right when he says that assigning a number to a trait like >colors is not correct. Also whether his concern over the variance values >is right? I agree with your colleague. Assigning a discrete number to a continuous trait would be permissible if the trait was numerical anyway and you were just generating classes of data and assigning the midpoint to each observation in a class. You have taken what is probably continuous data, categorized it, assigned arbitrary values to the classes, and then tried to do statistical analysis on the arbitrary values. Think what would happen to the statistics if you assigned values of 1, 10, 100, 1000, (or any other random set) to your color classes. The statistics obviously don't have much meaning. An alternative which MIGHT work is to assign color values based on the HSI (Hue, Saturation, Intensity) axes. After checking for obvious clustering of these color values, you may be able to look at the spread of values for each class you derive. But you may also find that there is no obvious separation of color values into well-defined classes. Try it. "You pays your money and you takes your choice." From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!CORNELL.EDU!MAL5 From: MAL5@CORNELL.EDU (Muhammad A. Lodhi) Newsgroups: bionet.molbio.rapd Subject: QTL analysis and variance of categorized data Date: 1 Jul 1994 08:12:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199407011512.LAA06568@postoffice.mail.cornell.edu> NNTP-Posting-Host: net.bio.net Dear Friends: I had a discussion with a colleague of mine about the QTL analysis (through MAPMAKER/QTL) of data that was divided into 4-5 categories instead of continuous figures. The data was related with, say fruit color. I divided the data into four arbitrary categories and gave a number to each category for analysis purposes, e.g., 1=green, 2=pinkish green, 3=brownish green and 4=purple. His concern is related with giving 1 to green, 4 to purple and so on. He says how can we say that green is 1 and not 4. In MAPMAKER/QTL we get variance explained for each QTL peak. My colleague says that variance can't be calculated in categorized data of a trait. My questions are; Whether he is right when he says that assigning a number to a trait like colors is not correct. Also whether his concern over the variance values is right? Any help will be highly appreciated. Muhammad A. Lodhi Cornell University From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!DEAKIN.EDU.AU!huangbx From: huangbx@DEAKIN.EDU.AU (huangbx) Newsgroups: bionet.molbio.rapd Subject: Minisatellate and microsatellate Date: 30 Jun 1994 21:28:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199407010428.OAA17900@sol.ccs.deakin.edu.au> NNTP-Posting-Host: net.bio.net Hello netters, What is the differences between minisatellate and microsatellate? With regards. Bixing Huang From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!PUCC.PRINCETON.EDU!FJUT042%TWNMOE10.BITNET From: FJUT042%TWNMOE10.BITNET@PUCC.PRINCETON.EDU (Josh Huang) Newsgroups: bionet.molbio.rapd Subject: How long is the DNA we shold have in the rapd reaction? Date: 30 Jun 1994 20:53:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199407010353.UAA22645@net.bio.net> NNTP-Posting-Host: net.bio.net Dear netter: Rogers said "DNA 50-100kb in length can be obten without great care being taken".(Plant Molcular Biology Manual A6: 1-10 (1988).) But how much infomation of the genome is there in the 50-100 kb fragements? Does it contrain the most of the pattens that we could obtain in the rapd reaction? If not, what length of the DNA we should have? Several days ago I got an info, it said that if the length of DNA is longer then 50 kb, the genome DNA that we seperated would carry above 99% of the inforamtions that genome should have. I do not know if it is right. If it is right, is there any reference? Any command is appreciated? Josh Huang Fu Jen Univesity Taiwan R.O.C. fjus243@twnmoe10.edu.tw From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!MERCURY.UARK.EDU!DRHOADS From: DRHOADS@MERCURY.UARK.EDU ("Doug Rhoads") Newsgroups: bionet.molbio.rapd Subject: Re: Minisatellite and microsatellite Date: 1 Jul 1994 06:39:23 -0700 Organization: University of Arkansas Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <127DA7D2993@uamercury.uark.edu> NNTP-Posting-Host: net.bio.net >In article <199407010428.OAA17900@sol.ccs.deakin.edu.au> huangbx@DEAKIN.EDU.AU ( >huangbx) writes: >>Hello netters, >>What is the differences between minisatellate and microsatellate? >>With regards. >>Bixing Huang >I do not claim to be the voice of authority, but here's what I've >seen in the literature. Microsatellites, also called simple >sequence repeats, are repeats of only a few bases, like two or three >or five or (maybe) ten. A typical microsatellite is the ubiquitous >CACA sequence. A block of microsatellite sequence usually contains >ten or more repeats. Minisatellites are larger, around a hundred up >to a few hundred base pairs. They are usually scattered through >the genome, not tandemly repeated. As far as I know, there is no >agreed upon size limit separating microsatellites from minis. >Most of the time the sequence fits in one group or the other. > >OK folks, so much for clearcut cases. Now here's a question: >How would you catagorize: > >A tandemly repeated sequence of about 150 bp containing within it >variable numbers of a tandemly repeated five bp sequence. > >A dispersed repeat of about 80 bp consisting mostly of a >conglomerate of 2 and 3 bp repeats. > >I've got 'em, but what are they? I would ditch the mini/micro since they seem to be becoming `dated'. Why not rely on the emerging acronyms Simple Sequence Repeats (SSR) and Simple Sequence Length Polymorphism (SSLP). Under this system they are both SSRs. Any one instance of an SSR may or may not be identified with an SSLP. 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 Jun 30 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!cat.cis.Brown.EDU!noc.near.net!bigboote.WPI.EDU!wpi.WPI.EDU!jbagshaw From: jbagshaw@wpi.WPI.EDU (Joseph C. Bagshaw) Newsgroups: bionet.molbio.rapd Subject: Re: Minisatellate and microsatellate Date: 1 Jul 1994 12:51:04 GMT Organization: Worcester Polytechnic Institute Lines: 38 Message-ID: <2v13fo$1tc@bigboote.WPI.EDU> References: <199407010428.OAA17900@sol.ccs.deakin.edu.au> NNTP-Posting-Host: wpi.wpi.edu In article <199407010428.OAA17900@sol.ccs.deakin.edu.au> huangbx@DEAKIN.EDU.AU (huangbx) writes: >Hello netters, > >What is the differences between minisatellate and microsatellate? > >With regards. > >Bixing Huang > I do not claim to be the voice of authority, but here's what I've seen in the literature. Microsatellites, also called simple sequence repeats, are repeats of only a few bases, like two or three or five or (maybe) ten. A typical microsatellite is the ubiquitous CACA sequence. A block of microsatellite sequence usually contains ten or more repeats. Minisatellites are larger, around a hundred up to a few hundred base pairs. They are usually scattered through the genome, not tandemly repeated. As far as I know, there is no agreed upon size limit separating microsatellites from minis. Most of the time the sequence fits in one group or the other. OK folks, so much for clearcut cases. Now here's a question: How would you catagorize: A tandemly repeated sequence of about 150 bp containing within it variable numbers of a tandemly repeated five bp sequence. A dispersed repeat of about 80 bp consisting mostly of a conglomerate of 2 and 3 bp repeats. I've got 'em, but what are they? -- ******************** HAVE GENES, WILL TRAVEL ******************** Joe Bagshaw, Worcester Polytechnic Institute jbagshaw@wpi.wpi.edu Roadkill on the information superhighway. From owner-rapd@net.bio.net Thu Jun 30 23:00:00 1994 Path: biosci!MED.PITT.EDU!rapr From: rapr@MED.PITT.EDU (Robert Preston) Newsgroups: bionet.molbio.rapd Subject: Re: Minisatellate and microsatellate (fwd) Date: 1 Jul 1994 13:04:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407012005.AA23052@deimos.med.pitt.edu> NNTP-Posting-Host: net.bio.net > > > >What is the differences between minisatellate and microsatellate? > > > > > I do not claim to be the voice of authority, but here's what I've > seen in the literature. Microsatellites, also called simple > sequence repeats, are repeats of only a few bases, like two or three > or five or (maybe) ten. A typical microsatellite is the ubiquitous > CACA sequence. A block of microsatellite sequence usually contains > ten or more repeats. Minisatellites are larger, around a hundred up >[more edits] > OK folks, so much for clearcut cases. Now here's a question: > How would you catagorize: > > A tandemly repeated sequence of about 150 bp containing within it > variable numbers of a tandemly repeated five bp sequence. > Nested CA-CA? > A dispersed repeat of about 80 bp consisting mostly of a > conglomerate of 2 and 3 bp repeats. > 'Pends on what the repeats are. Could be a CA-CA, GAG, GAG motif? > I've got 'em, but what are they? > Dunno. But recommend against taste-testing (seriously). > > > -- > ******************** HAVE GENES, WILL TRAVEL ******************** > Joe Bagshaw, Worcester Polytechnic Institute > jbagshaw@wpi.wpi.edu > Roadkill on the information superhighway. > Rob rapr@med.pitt.edu