From owner-genome-program@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Victor Solovyev Newsgroups: bionet.molbio.genome-program Subject: Blastp search in Human Predicted Genes and Proteins Database Date: 2 Oct 1998 15:18:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 87 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <6v3jfr$en0@net.bio.net> NNTP-Posting-Host: net.bio.net Blastp search in DB of Human Predicted Genes and Proteins ------------------------------------------------------------------ We install NCBI's Gapped BLASTP search in Database of protein sequences of predicted genes (INFOGENEP) of finished and unfinished human sequences at http://genomic.sanger.ac.uk/db.html Web page of Computational Genomic Group of the Sanger Centre. If you find some interesting similarity with your sequence you can use ID to check the gene structure of this protein in the INFOGENP DB and get clone name and sequence Example: ============== a sequence T0078 from CASP3 has significan similarity with protein of predicted gene GHS005230 from clone dJ337O18 of Sanger finished sequences Query= Query: (288 letters) Database: INFOGENE_PREDICTIONS 18,574 sequences; 3,010,387 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ID GHS005230 dJ337O18 human_pg Sanger_finished 319 212 8e-56 ID GHS005240 dJ337O18 human_pg Sanger_finished 477 124 2e-29 >ID GHS005230 dJ337O18 human_pg Sanger_finished 319 Length = 319 Score = 212 bits (533), Expect = 8e-56 Identities = 120/282 (42%), Positives = 167/282 (58%), Gaps = 10/282 (3%) Query: 12 TLLNLEKIEEGLFRGQSEDLGLRQVFGGQVVGQALYAAKETVPEERLVHSFHSYFLRPGD 71 T+LNLE ++E LFRG+ + +++FGGQ+VGQAL AA ++V E+ VHS H YF+R GD Sbjct: 30 TVLNLEPLDEDLFRGRHYWVPAKRLFGGQIVGQALVAAAKSVSEDVHVHSLHCYFVRAGD 89 Query: 72 SKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASF-QAPEAGFEHQKTMPSAPAPD 130 K P++Y VE R G+SFS R V A+Q+GKPIF ASF QA + +HQ +MP+ P P+ Sbjct: 90 PKLPVLYQVERTRTGSSFSVRSVKAVQHGKPIFICQASFQQAQPSPMQHQFSMPTVPPPE 149 Query: 131 G-LPSETQIAQ-----SLAHLLPPVLKDKFICDRPLEVRPVEFHNPLKGHVAEPHRQVWI 184 L ET I Q +L P L + P+E++PV + EP + W+ Sbjct: 150 ELLDCETLIDQYLRDPNLQKRYPLALNRIAAQEVPIEIKPVNPSPLSQLQRMEPKQMFWV 209 Query: 185 RANGSVPD-DLRVHQYLLGYASDLNFLPVALQPHGIGFLEPGIQIATIDHSMWFHRPFNL 243 RA G + + D+++H + Y SD FL AL PH + + ++DHSMWFH PF Sbjct: 210 RARGYIGEGDMKMHCCVAAYISDYAFLGTALLPH--QWQHKVHFMVSLDHSMWFHAPFRA 267 Query: 244 NEWLLYSVESTSASSARGFVRGEFYTQDGVLVASTVQEGVMR 285 + W+LY ES A +RG V G + QDGVL + QEGV+R Sbjct: 268 DHWMLYECESPWAGGSRGLVHGRLWRQDGVLAVTCAQEGVIR 309 ----------------------------------------------- Currently DB includes genes predicted for Sanger finished and unfinished sequences. It is about 1500 locuses and 18000 protein sequences corresponding predicted genes (by Fgenes and Genescan programs). Exons predicted by both programare much more often the real ones. Known Protein and EST similarity included in the data. This DB will include all predicted genes and protein for the Human genome draft as well as genes and proteins predicted for other model organisms. The database list: Predicted GENES Structure Database (INFOGENEP Rel 1.) Nucleotide and Protein sequences of INFOGENEP genes GENES Structure and Functioning Database (INFOGENE Rel 1.) Nucleotide and Protein sequences of INFOGENE genes -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-genome-program@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!biosci!not-for-mail From: guo@badlands.NoDak.edu (Yonghong Guo) Newsgroups: bionet.molbio.genome-program Subject: sequence homology Date: 5 Oct 1998 14:36:38 -0700 Organization: North Dakota Higher Ed. Network Lines: 14 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <6vbe56$ig9@net.bio.net> NNTP-Posting-Host: net.bio.net I am currently working on a sequence project on ribosomal RNA genes. I am trying to compare the sequence from my species with known sequences from other species. What I am looking for is: any recommendations on software or methods to calculate the homology between two sequences? Any suggestion is appreciated. Yonghong Guo Dept. Plant Sciences North Dakota State University Fargo, ND 58105 701-231-8473 From owner-genome-program@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Victor Solovyev Newsgroups: bionet.molbio.genome-program Subject: New Prediction of Variants of gene structure FGENES-M Date: 5 Oct 1998 14:36:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 180 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <6vbe56$igb@net.bio.net> NNTP-Posting-Host: net.bio.net New Prediction of Variants of gene structure FGENES-M ====================================================== Fgenes-M variant for mammalian sequences is available at CGG WEB site: http://genomic.sanger.ac.uk/gf/gf.html There are 2 reasons to predict several sub-optimal variants of gene structure (instead of only one): 1) Gene prediction algorithms for long genomic sequences are just 70-80% accurate in average, therefore a real structure might have the score slightly lower than the produced optimal variant (and you will never see it for such case having just 1 prediction); 2) Mammalian genes often have alternative splicing and your sequenced mRNA might not correspond to the predicted variant (in this case actually several gene structures are real). There are thousands of alternative gene structures is possible to generate and currently does not exist established way to generate variants exactly corresponding to the real ones. Fgenes-M variant (fgenem) was proved to be useful in helping provide a set of possible gene structures for further experimental testing in commercial gene hunting, therefore I decided to put it to WWW. FGENES-M 1.5 - Pattern based Human Multiple variants of Gene structure prediction Algorithm outputs several suboptimal variants of predicted gene structure. In the current WWW server variant up to 10 structures of gene of multiple genes is provided. It is similar with FGENES and based on pattern recognition of different types of exons, promoters and polyA signals and by dynamic programming finding the optimal combination of them constructing a set of gene models along a given sequences You might compare a validity of a predicted variant using GENE WEIGHT, if it is close to the 1st optimal variant, than it worth to consider it. A simple example of Fgenes-M output: FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 1 Max var= 5 GENE WEIGHT: 24.1 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 369 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTVFACFAAANPGY AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKVDDGSELSSTSRTEVSS VSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 2 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 3 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 4 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 5 Max var= 5 GENE WEIGHT: 13.9 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3668 0.99 3558 - 3668 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 326 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTFRNCIMQLFGKK VDDGSELSSTSRTEVSSVSNSSVSPA -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-genome-program@net.bio.net Wed Oct 14 23:00:00 1998 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov (Betty K Mansfield) Newsgroups: bionet.molbio.genome-program Subject: DNATools Info Date: 15 Oct 1998 12:54:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 87 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <705jtc$dnb@net.bio.net> NNTP-Posting-Host: net.bio.net --- Forwarded message follows --- From: "Søren W. Rasmussen" Subject: DNATools Info Date: 12 Oct 1998 11:35:29 -0700 **************************************************************************** NEW in revision 112: Revision 112 includes an new function for automated mail blast search. Simply load your sequences into a project and start the mail blast search. DNATools will then send your sequences as e-mails to a mail blast server (e.g. NCBI), wait until the result is returned to your mailbox and finally build the search data into the sequence header of your files. **************************************************************************** Dear DNATools user, As I have indicated in my previous notes, DNATools has been used by a number of people, including myself during several years. This implies that the various functions of the program have been continuously tested by scientists actually working with sequences. As a result, I have recieved many comments and suggestions from a fairly large group of end-users. Unlike most commercial programs, my ambition has been to make corrections and improvements to DNATools whenever someone draws my attention to a bug, a correction or an improvement. The program is then compiled and the new revision made available to all users. A drawback of this policy is of course that the number of updates is large - and that many users have different versions/revisions which makes it difficult for me to comment on errors in older versions. The advantage, on the other hand, is that users get immediate response to their suggestions and bug reports. People that don't want to continuously download new updates are obviously free to stick to the version they already have. For those of you that don't like bugs, please compare the version and revision number of your copy with the files located at: ftp://ftp.crc.dk/pub/dnatools 51112_EXE.ZIP contains the most recent exe and hlp files. DT_51112.ZIP contains the most recent complete setup. to see if a newer version and/or revision is available. Replace your current copy with the latest update and check if the problem still persists. If it does then contact me at swr@crc.dk Re-installation is normally not necessary if you just replace the exe and help files. In case you experience problems starting and/or running DNATools after replacing the two files, your installation is probably too old and you have to run a complete setup. If you are interested in being kept informed directly about the life of DNATools, please send your name and e-mail address to swr@crc.dk. Best regards Soeren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 3327 5230 / 45 3616 2259, Fax 45 3327 4766 E-mail swr@crc.dk From owner-genome-program@net.bio.net Wed Oct 14 23:00:00 1998 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov Newsgroups: bionet.molbio.genome-program Subject: AVAILABILITY OF FELLOWSHIPS FOR GENOMIC ANALYSIS--NEXT RECEIPT D ATE Date: 15 Oct 1998 12:54:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <705jtc$dn9@net.bio.net> NNTP-Posting-Host: net.bio.net ------- Forwarded Message Date: Thu, 01 Oct 1998 07:43:09 -0400 From: "Graham, Bettie (NHGRI)" Subject: AVAILABILITY OF FELLOWSHIPS FOR GENOMIC ANALYSIS--NEXT RECEIPT D ATE IS DECEMBER 5, 1998 ____________________________________________________________________________ The National Human Genome Research Institute, National Institutes of Health, is offering individual fellowships to highly qualified students and scientists who are seeking training that will enable them to engage in research relevant to the Human Genome Project. Training of scholars in examining the ethical, legal and social Implications of human genome research is also encouraged, but is not available for pre-doctoral students. Three types of fellowships are offered: 1. Postdoctoral fellowships for indivduals who have received their doctoral degree within the last seven years. The application receipt dates are, December 5 and April 5, and August 5. 2. Senior postdoctoral fellowships for individuals who received their doctoral degree more than seven years ago. The application receipt dates are, December 5 and April 5, and August 5. 3. Pre-doctoral Minority fellowships for graduate students with disabilities and underrepresented minority graduate students to pursue a doctoral degree. The application receipt dates are November 15 and May 1. Fellowship support is provided through the National Research Service Award. Only U.S. citizens or permanent residents of the United States are eligible to apply. Minorities, women and individuals with disabilities are encouraged to apply. For additional information about fellowship opportunities available through the NCHGR, please visit our home page at: http://www.nhgri.nih.gov/Grant_info/Funding/Training . You may also contact the following staff: Individual and Senior Postdoctoral Fellowships and Minority Pre-Doctoral Fellowships in Genomic Analysis and Technology: Bettie J. Graham, Ph.D.. TEL: (301) 496-7531 e-mail: bettie_graham@nih.gov Individual and Senior Postdoctoral Fellowships in ELSI Topics: Elizabeth Thomson, M.S., R.N. TEL: (301) 402-4997 e-mail: elizabeth_thomson@nih.gov For information about PHS Grant Policy, applicants may contact: Ms. Jean Cahil TEL: (301) 402-0733 e-mail: jean_cahill@nih.gov ------- End of Forwarded Message From owner-genome-program@net.bio.net Thu Oct 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: FlyBase jobs available Newsgroups: bionet.molbio.genome-program Subject: FlyBase Employment Opportunities Date: 23 Oct 1998 09:14:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <70qa1e$76o@net.bio.net> NNTP-Posting-Host: net.bio.net =============================================================== *EMPLOYMENT OPPORTUNITIES IN FLYBASE* During the next few months, FlyBase expects to have several new positions for scientific curators/indexers and computer scientists/applications programmers. With new funding, we expect that the FlyBase Consortium will consist of about 30 scientists located at four sites (Harvard University, University of California, Berkeley, Indiana University and the University of Cambridge). These FlyBase positions include: Location Position Harvard University Full-time Scientific curator/indexer Indiana University Full-time Computer scientist/application programmer U. of Cambridge (UK) Full-time Scientific curator/indexer U.C. Berkeley Full-time Database/Bioinformatics Computer Scientist To learn more about these openings and how to apply, go to the FlyBase home page (http://flybase.bio.indiana.edu/) or to the nearest FlyBase mirror site and click on the "FlyBase Job Openings" hyperlink in the General Information list located in the home page sidebar. =============================================================== From owner-genome-program@net.bio.net Thu Oct 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Betty K Mansfield Newsgroups: bionet.molbio.genome-program Subject: DOE Joint Genome Institute Exceeds Sequencing Goal Date: 23 Oct 1998 11:21:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <70qhf8$qsi@net.bio.net> NNTP-Posting-Host: net.bio.net US Department of Energy Joint Genome Institute Exceeds DNA Sequencing Goal The DOE Joint Genome Institute (JGI) surpassed its ambitious goal of sequencing 20 million base pairs of human DNA for fiscal year 1998. The achievement, which marks a ten-fold increase in production output over the previous year, distinguishes the JGI as a major contributor of human DNA sequence to worldwide public databases. http://www.lbl.gov/Science-Articles/Archive/20-million-bases.html The JGI, established in 1996, is a consortium of scientists, engineers and support staff from the Department of Energy's Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Laboratories. http://www.ornl.gov/hgmis/publicat/hgn/v8n2/01doe.html The DOE HGP is a program in the Office of Biological and Environmental Research's Health Effects and Life Sciences Research Division. http://www.er.doe.gov/production/ober/ober_top.html From owner-genome-program@net.bio.net Thu Oct 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Betty K Mansfield Newsgroups: bionet.molbio.genome-program Subject: Human Genome Project New Five Year Plan Date: 23 Oct 1998 11:23:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <70qhj0$r4r@net.bio.net> NNTP-Posting-Host: net.bio.net New Roadmap for U.S. Human Genome Project (HGP) Published in Science Today DOE and NIH presented a new plan outlining HGP goals for the next five years. The plan, which covers fiscal years 1999-2003, calls for production of a "working draft" of the human genome by 2001 and a complete and accurate sequence by 2003, two years ahead of the originally scheduled completion date of 2005. A detailed article whose authors include HGP directors Ari Patrinos (DOE) and Francis Collins (NIH) explaining the new HGP goals appears in the 23 October 1998 issue of Science. For more information please see: http://www.ornl.gov/hg5yp http://www.nhgri.nih.gov/ http://www.sciencemag.org/content/vol282/issue5389/ From owner-genome-program@net.bio.net Mon Oct 26 22:00:00 1998 Path: biosci!biosci!not-for-mail From: Virginia Urquidi Newsgroups: bionet.molbio.genome-program Subject: To identify human DNA in a mouse DNA background. What is best? Date: 27 Oct 1998 07:07:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <714nk9$fan@net.bio.net> NNTP-Posting-Host: net.bio.net I have "inherited" a project where human DNA was identified against a mouse background by BLUR8 hybridization. Analysis of one of the DNA cloned fragments reveals the presence of an intron which I can amplify from mouse genomic DNA but not from human DNA. Because there are 3 small regions of homology (~20bp) between BLUR8 and the clone I assume the false identification was due to low stringency hybridization. Since it seems I will have to start the process again, my questions for those experienced in the field are: 1) Is the use of BLUR8 advisable for this purpose? One of its drawbacks seems to be mismatch with the majority of Alu repeats. 2) Is the Alu consensus clone pPD39 (GATA 11:34,1994) a better probe? 3) Can I use human Cot-1 DNA ? If so, is the one sold by GIBCO/BRL any good? 4) Any other approach recommended? Grateful for your answers V. Urquidi vurquidi@ucsd.edu ____________________________________________________________ Dr. Virginia Urquidi UCSD Cancer Center 9500 Gilman Drive, CMM East La Jolla, CA 92093-0684 Tel: (619) 822 2082 Fax: (619) 822 2084 ____________________________________________________________ From owner-genome-program@net.bio.net Thu Oct 29 22:00:00 1998 Path: biosci!biosci!not-for-mail From: CPK@leicester.ac.uk Newsgroups: bionet.molbio.genome-program Subject: Euroneurofly 2000, Alicante, Spain Date: 30 Oct 1998 15:35:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <71digc$7u6@net.bio.net> NNTP-Posting-Host: net.bio.net Hi all, just as we put the lid on the 1998 Euroneurofly meeting in Warwick UK last month, with that wonderful last night at the Monastery, the next one looms on the horizon. The millenium meeting will be in Alicante, Spain and will be organised by Francisco (Paco) Tejedor and Fernando Jimenes. the timing will be either September or December, and Paco tells me he will be in touch with you all in due course to consult you on what dates are most suitable. Note that Paco's email is f.tejedor@umh.es Best wishes Bambos Kyriacou Warwick Neurofly co-organiser