Path: utzoo!utgpu!water!watmath!uunet!ig!daemon From: MJB1@VMS-SUPP.CAM.AC.UK Newsgroups: bionet.molbio.seqnet Subject: SEQNET Bulletin Message-ID: <5189@ig.ig.com> Date: 18 Feb 88 14:03:34 GMT Sender: daemon@presto.ig.com Lines: 150 From: MJB1@VMS-SUPP.CAM.AC.UK Bulletin_# 83 17-FEB-1988 15:21 GenB From: Date: 17-FEB-1988 15:21 To: SEQNET Subject: GenBank changes Via: UK.AC.RL.EARN; Wed, 17 Feb 88 15:20:28 GMT Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 0023; Wed, 17 Feb 88 15:20:28 GM Received: from IBOINFN.BITNET by UKACRL.BITNET (Mailer X1.25) with BSMTP id 0001; Wed, 17 Feb 88 15:20:26 Date: Wed, 17 Feb 88 13:31 N From: Reply-To: Subject: GenBank changes To: MJB1@UK.AC.CAM.VMS-SUPP X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK" Message-id: <6589> Date: WED, 17-FEB-88 13:31 N From: Reply-To: (alternate reply) Subject: GenBank changes To: X-Original-To: mjb1@vms-supp.cam.ac.uk, ATTIMONELLI Christian Burks: we refer to our previous communication about GenBank changes and your answer dated 6-Feb-1988. We still believe that it is very important to have the collections structured in such a way to maintain the maximum information in a machine readable form allowing a selective retrieval. You stated in your message that since you "are not able to automatically translate" EMBL features into GenBank format "you decided to adopt" the use of COMMENT field for parking EMBL feature. This, together with the lost of the SITES field, is in our opinion a great devaluation of the GenBank collection and in particular makes the GenBank unusable for our software ACNUC. We have the software TRANSFORM which automatically convert in all its part the EMBL collection into the "old" GenBank format. An example is reported below refering to the EMBL entry PTAGGLOG already mentioned in our previous message. If you are interested in the software TRANSFORM please contact us at your earlier convenience. Dr. Marcella Attimonelli >>>>>>>>>> EMBL PTAGGLOG entry converted into GenBank format by TRANSFORM program LOCUS PTAGGLOG 1815 bp DNA entered 02/16/87 DEFINITION Chimpanzee fetal A-gamma-globin gene ACCESSION X03110 KEYWORDS gamma-globin; A-gamma-globin; direct repeat; tandem repeat. SOURCE ORGANISM Pan troglodytes ;(chimpanzee, chimpanze, Chimpanse) Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia; Eutheria; Primates. REFERENCE 1 (bases 1 to 1815) AUTHORS Slightom,J.L., Chang,L.-Y.E., Koop,B.F. and Goodman,M. TITLE Chimpanzee fetal G-gamma and A-gamma globin gene nucleotide sequences provide further evidence of gene conversions in hominine evolution JOURNAL Mol. Biol. Evol. 2, 370-389 (1985) COMMENT History: 17-JAN-1986 (annotation) Data kindly reviewed (07-JUL-1986) by Slightom J.L. FEATURES from to/span description pept 55 199 put. exon 1 matp 108 199 A-gamma-globin (aa 1-31) (199 is 2nd base in codon) 322 544 A-gamma-globin (aa 32-105) (322 is 3rd base in codon) 1432 1557 A-gamma-globin (aa 106-147) pept 1431 1647 put. exon 3 RNA 55 1647 put. primary transcript SITES ->prm 24 1 put. TATA-box start prm<- 28 1 put. TATA-box end cap 55 0 put. cap site ->pept 55 1 put. exon 1 start ->RNA 55 1 put. primary transcript start ->matp 108 1 A-gamma-globin (aa 1-31) (199 is 2nd base in codon) start matp/ivs 199 0 A-gamma-globin (aa 1-31) (199 is 2nd base in codon) end/intron start pept<- 199 1 put. exon 1 end ivs/matp 322 0 intron end /A-gamma-globin (aa 32-105) (322 is 3rd base in codon) start matp/ivs 544 0 A-gamma-globin (aa 32-105) (322 is 3rd base in codon) end/intron start ->rpt 1123 1 TG(14) repeat (hot spot sequence start rpt<- 1162 1 TG(14) repeat (hot spot sequence end ->pept 1431 1 put. exon 3 start ivs/matp 1432 0 intron end /A-gamma-globin (aa 106-147 ) start matp<- 1557 1 A-gamma-globin (aa 106-147) end ->site 1621 1 put. polyadenylation signal start site<- 1626 1 put. polyadenylation signal end polya 1647 0 put. polyadenylation site pept<- 1647 1 put. exon 3 end RNA<- 1647 1 put. primary transcript end BASE COUNT 471 A 357 C 474 G 513 T ORIGIN 1 CCGGCGGCTG GCTAGGGATG AAGAATAAAA GGAAGCACCC TCCAGCAGTT CCACACACTC 61 GCTTCTGGAA CGTCTGAGGT TATCAATAAG CTCCTAGTCC AGACGCCATG GGTCATTTCA 121 CAGAGGAGGA CAAGGCTACT ATCACAAGCC TGTGGGGCAA GGTGAATGTG GAAGATGCTG 181 GAGGAGAAAC CCTGGGAAGG TAGGCTCTGG TGACCAGGAC AAGGGAGGGA AGGAAGGACC 241 CTGTGCCTGG CAAAAGTCCA GGTCACTTCT CAGGATTTGT GGCACCTTCT GACTGTCAAA 301 CTGTTCTTGT CAATCTTACA GGCTCCTGGT TGTCTACCCA TGGACCCAGA GGTTCTTTGA 361 CAGCTTTGGC AACCTGTCCT CTGCCTCTGC CATCATGGGC AACCCCAAGG TCAAGGCACA 421 TGGCAAGAAG GTGCTGACTT CCTTGGGAGA TGCCATAAAG CACCTGGATG ACCTCAAGGG 481 CACCTTTGCC CAGCTGAGTG AACTGCACTG TGACAAGCTG CATGTGGATC CTGAGAACTT 541 CAAGGTGAGT CCAGGAGATG TTTCAGCCCT GTTGCCTTTA GTCTGGAGGC AACTTAGACA 601 ACTGAGTATT AATCTGAGCA CAGCTGAATC TACCCACAGG GTGTAAACTA TTTGAAGATA 661 TTGGGGTTGG GAGTGAAGGA ACTGCAGAGG ACTAACTGGG CTGAGACCCA GTGGTAATGT 721 TTTAGGGCCT AAGGAGTGCC TCTAAAAATC TAGATGGACA ATTTTGACTT TGAGAATAGA 781 GAGGTGGAAA TGAGGAAAAT GACTTTTCTT TATTAGATTC CAGTAGAAAG AACTTTCATC 841 TTTCCCTCAT TTTTGTTGTT TTAAAACATC TATCTGGAGG CAGGACAAGT ATGGTCATTA 901 AAAAGATGCA GGCAGAAGGC ATATATTGGC TCAGTCAAAG TGGGGAACTT TGGTGGCCAA 961 ACATATATTG CTAAGGCTAT TCCTATGTCA TCTGGACACA TATAAAATGC TGCTAATGCT 1021 TCATTACAAA CTTATATCCT TTAATTCCAG ATGGGGGCAA AGTATGTCCA GGGGTGAGGA 1081 ACAATTGGAA CATTTGGGCT GGAGTAGATT TTGAAAGTCA GCTGTGAGTT TGTGTGTGTG 1141 TGTGTGTGTG TGTGTGTGCG TGTCAGCGTG TGTTTCTTTT AACGTCTTCA GCCTACAACA 1201 TACAGGGTTC ATGGTGGCAA GAAGATAGCA AGATTTAAAT TATGGCCAGT GACTAGTGCT 1261 GCAAGGGGAA CAACTACCTG CATTTAATGG GAAGGCAAAA TCTCAGGCTT TGAGGGAAGT 1321 TAACATAGGC TTGATTCTGG GTGGAAGCTG GGTGTGTAGT TATCTGGAGG CCAGGCTGGA 1381 GCTCTCAGCT CACTATGGGT TCATCTTTAT TGTCTCCTTT CATCTCAACA GCTCCTGGGA 1441 AATGTGCTGG TGACCGTTTT GGCAATCCAT TTCGGCAAAG AATTCACCCC TGAGGTGCAG 1501 GCTTCCTGGC AGAAGATGGT GACTGCAGTG GCCAGTGCCC TGTCCTCCAG ATACCACTGA 1561 GCCTCTTGCC CATGATTCAG AGCTTTCAAG GATAGGCTTT ATTCTGCAAG CAATACAAAT 1621 AATAAATCTA TTCTGCTGAG AGATCACACA TGATTTTCTT CAGCTCTTTT TTTTACATCT 1681 TTTTAAATAC ATGAGCCACA AAGGGTTTAT ATTGAGGGAA GTGTGTATGT GTATTTCTGC 1741 ATGCCTGTTT GTGTTTGTGG TGTGTGCATG CTCCTCATTT ATTTTTATAT GAGATGTGCA 1801 TTTTGATGAG CAAAT //