P9323611%ARIZRVAX@PUCC.PRINCETON.EDU (02/14/91)
I a medical student at the University of Arizona and I am doing research involving gene amplification of the human collagenase IV gene. Could you please send me information concerning your Human GENE Database(i.e. is there some way I can get connect to the GENEBANK database so that I can search for my gene sequence? Is there a manual I might need? Thanks for your time and help, John Pierpont
kristoff@GENBANK.BIO.NET (Dave Kristofferson) (02/15/91)
> > I a medical student at the University of Arizona and I am doing research > involving gene amplification of the human collagenase IV gene. Could you > please send me information concerning your Human GENE Database(i.e. is there > some way I can get connect to the GENEBANK database so that I can search for > my gene sequence? Is there a manual I might need? > > Thanks for your time and help, > John Pierpont > > To obtain instructions for doing GenBank searches by e-mail send a message containing the word HELP to search@genbank.bio.net I include information about the GenBank On-line Service below which allows you more extensive access to the database. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net ---------------------------------------------------------------------- GenBank On-line Service Features ------------------------------------ **** New Solbourne Computer A powerful 80 MIPS (million instructions per second) Solbourne superminicomputer is used for all aspects of the GenBank On-line service. A 1000 base query sequence can be compared against all of GenBank in about 12 minutes using the FASTA similarity searching program (see below). **** Daily Updates of the GenBank, GenPept, and EMBL Databases Users can now retrieve and search the latest GenBank and EMBL sequence entries. A database (GenPept) containing translations of all annotated open reading frames in GenBank is also available. "New" databases of recent GenBank, GenPept, and EMBL entries are updated daily with data supplied by Los Alamos National Laboratory and the EMBL. Both the IRX and FASTA programs search these new entries. **** Fast, Indexed, Annotation Search and Entry Retrieval The IRX software from the National Library of Medicine is used to provide fast retrieval of database entries by any combination of words within the entry annotations. Sequences identified by the program may then be downloaded using the Kermit protocol or saved to the user's directory. **** Similarity Searching Using FASTA All of the above databases may be searched using the FASTA program written by William Pearson. The TFASTA program which compares protein sequences to the nucleic acid databases in up to 6 reading frames by translating at runtime is also available. **** Electronic Communications and Bulletin Boards (Newsgroups) Users with accounts on the GenBank On-line Service computer can use its electronic mail facilities to communicate at no cost with colleagues worldwide. Access to the numerous USENET newsgroups is available. Questions on a wide variety of subjects can be posted for an international audience. Of primary interest for the GenBank community are the BIOSCI newsgroups which cover subjects such as laboratory methods, journal contents, protein analysis, NIH funding announcements, and biological software. **** Access to the IntelliGenetics Suite of Programs For an additional fee, Class II users will also have access to all of the IntelliGenetics Suite of molecular biology sequence analysis software and the databases which are distributed with that software. This software provides a comprehensive range of functionality and is described in a separate enclosure. **** Connection by Public Data Network or by Internet The GenBank On-line Service computer can be accessed by the SprintNet Public Data Network using a modem and phone lines or, for users that have an account on a computer with access to the Internet, by interactive connection using the TELNET protocol. User Class Descriptions ----------------------- Two different classes of login accounts exist on the GenBank computer and are referred to as Class I and Class II accounts as described below. In addition certain services are provided at no charge for the community at large through either anonymous login to the GenBank computer or by electronic mail server. Both non-profit AND for-profit users may access the GenBank On-line Service. The same fee structure applies to both types of users (contact us as indicated below for details). >>>> Services available to Class I (basic) time-sharing accounts ** Private login account with 1 Mbyte disk space. ** Daily database updates. ** Unrestricted access to databases through the IRX program. ** Interactive and batch use of FASTA and TFASTA similarity search programs. ** Access to worldwide electronic mail communication and all USENET newsgroups including the 18 BIOSCI (bionet.*) newsgroups specializing in topics for molecular biologists. >>>> Services available to Class II time-sharing accounts ** All of the Class I services. ** Access to all IntelliGenetics Suite programs and databases. >>>> Services available at no cost **Limited 20 min. IRX sessions to download database entries.** To use this anonymous access, dial 415-961-6860 for 1200 or 2400 baud access (415-961-6864 for 9600 baud Telebit Trailblazer access). Then use the GenBank username "genbank" with the password "4nigms" to log into the public account. You will be placed into the IRX program automatically. Access is also possible by the Internet. "TELNET" to the computer "genbank.bio.net" and log in with the GenBank username and password given above. **FASTA similarity searching by electronic mail.** To get instructions for using the FASTA Server, send an e-mail message with the command "help" in the body of the message to the Internet address "search@genbank.bio.net". **Sequence retrieval by locus name or accession number through an electronic mail server.** Instructions are available by sending a message similar to the above to the address retrieve@genbank.bio.net. **Daily/Weekly updates of GenBank, GenPept, and EMBL by anonymous FTP.** For further information please call GenBank at 415-962-7364, send e-mail to gos@genbank.bio.net, or write us at GenBank On-line Service c/o IntelliGenetics, Inc. 700 E. El Camino Real Mountain View, CA 94040 U.S.A.
B_FOLEY%UVMVAX@PUCC.PRINCETON.EDU (02/16/91)
I hope this is all you needed. If not, write back to: B_FOLEY@UVMVAX.BITNET Brian Foley; Graduate student, U of Vermont ------------------------------------------------------------------------- ! STRINGS from: GenEMBL:* February 15, 1991 10:55 ! searching for: "collagenase" .. OM:Rabcn1 M17820 Rabbit collagenase gene, exon 1. 6/88 718bp OM:Rabcn2 M17821 Rabbit collagenase gene, exons 2, 3, and 4. 6/88 1,0 57bp OM:Rabcn3 M17822 Rabbit collagenase gene, exons 5 and 6. 6/88 831bp OM:Rabcn4 M19240 Rabbit collagenase gene, exons 7 and 8. 6/88 297bp OM:Rabcn5 M17823 Rabbit collagenase gene, exons 9 and 10. 6/88 919bp Pr:Hum4cola J05070 Human type IV collagenase mRNA, complete cds. 3/90 2 ,334bp Pr:Humcn2 M13509 Human skin collagenase mRNA, complete cds. 2/87 1,97 0bp Pr:Humcn25 M15996 Human synovial cell collagenase mRNA. 3/88 261bp Pr:Humcn2a M16567 Human collagenase gene, 5' end. 6/89 698bp Pr:Humcn4gel J03210 Human collagenase type IV mRNA, 3' end. 12/88 2,733b p Pr:Humcollr X05231 Human mRNA for collagenase (E.C. 3.4.24). 6/88 1,968 bp Pr:Humfci M12670 Human fibroblast collagenase inhibitor mRNA, complet e cds. 3/89 769bp Pr:Humpump1 X07819 Human pump-1 mRNA homolog to metalloproteinase, coll agenase and stromelysin. 9/89 1,078bp Pr:Humsccasa M25663 Human synovial cell collagenase mRNA, 3' end. 9/89 5 13bp EM:Hsclg4 M33789 Human type-4 collagenase (CLG4) preproenzyme gene, e xon 1. 4/90 451bp EM:Ssmmp1 X54724 Porcine mmp1 mRNA for matrix metalloproteinase (type I collagenase) (EC 3.4.24.7). 11/90 1,33 ! Sequences searched: 45153 LOCUS HUM4COLA 2334 bp ss-mRNA PRI 15-MAR-1990 DEFINITION Human type IV collagenase mRNA, complete cds. ACCESSION J05070 KEYWORDS collagenase; metalloprotease. SOURCE Human lung fibroblast cDNA to mRNA. ORGANISM Homo sapiens Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia; Theria; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae. REFERENCE 1 (bases 1 to 2334) AUTHORS Wilhelm,S.M., Collier,I.E., Marmer,B.L., Eisen,A.Z., Grant,G.A. and Goldberg,G.I. TITLE SV40-transformed human lung fibroblasts secrete a 92-kDa type IV collagenase which is identical to that secreted by normal human macrophages JOURNAL J. Biol. Chem. 264, 17213-17221 (1989) STANDARD simple staff_review FEATURES Location/Qualifiers CDS 20. .2143 /note="92 kDa type IV collagenase /map='16q21' /hgml_locus_uid='LJ0160L'" /gene="CLG4" BASE COUNT 412 a 760 c 697 g 465 t ORIGIN Pr:Hum4cola Length: 2334 February 15, 1991 10:57 Check: 644 .. 1 AGACACCTCT GCCCTCACCA TGAGCCTCTG GCAGCCCCTG GTCCTGGTGC 51 TCCTGGTGCT GGGCTGCTGC TTTGCTGCCC CCAGACAGCG CCAGTCCACC 101 CTTGTGCTCT TCCCTGGAGA CCTGAGAACC AATCTCACCG ACAGGCAGCT 151 GGCAGAGGAA TACCTGTACC GCTATGGTTA CACTCGGGTG GCAGAGATGC 201 GTGGAGAGTC GAAATCTCTG GGGCCTGCGC TGCTGCTTCT CCAGAAGCAA 251 CTGTCCCTGC CCGAGACCGG TGAGCTGGAT AGCGCCACGC TGAAGGCCAT 301 GCGAACCCCA CGGTGCGGGG TCCCAGACCT GGGCAGATTC CAAACCTTTG 351 AGGGCGACCT CAAGTGGCAC CACCACAACA TCACCTATTG GATCCAAAAC 401 TACTCGGAAG ACTTGCCGCG GGCGGTGATT GACGACGCCT TTGCCCGCGC 451 CTTCGCACTG TGGAGCGCGG TGACGCCGCT CACCTTCACT CGCGTGTACA 501 GCCGGGACGC AGACATCGTC ATCCAGTTTG GTGTCGCGGA GCACGGAGAC 551 GGGTATCCCT TCGACGGGAA GGACGGGCTC CTGGCACACG CCTTTCCTCC 601 TGGCCCCGGC ATTCAGGGAG ACGCCCATTT CGACGATGAC GAGTTGTGGT 651 CCCTGGGCAA GGGCGTCGTG GTTCCAACTC GGTTTGGAAA CGCAGATGGC 701 GCGGCCTGCC ACTTCCCCTT CATCTTCGAG GGCCGCTCCT ACTCTGCCTG 751 CACCACCGAC GGTCGCTCCG ACGGCTTGCC CTGGTGCAGT ACCACGGCCA 801 ACTACGACAC CGACGACCGG TTTGGCTTCT GCCCCAGCGA GAGACTCTAC 851 ACCCGGGACG GCAATGCTGA TGGGAAACCC TGCCAGTTTC CATTCATCTT 901 CCAAGGCCAA TCCTACTCCG CCTGCACCAC GGACGGTCGC TCCGACGGCT 951 ACCGCTGGTG CGCCACCACC GCCAACTACG ACCGGGACAA GCTCTTCGGC 1001 TTCTGCCCGA CCCGAGCTGA CTCGACGGTG ATGGGGGGCA ACTCGGCGGG 1051 GGAGCTGTGC GTCTTCCCCT TCACTTTCCT GGGTAAGGAG TACTCGACCT 1101 GTACCAGCGA GGGCCGCGGA GATGGGCGCC TCTGGTGCGC TACCACCTCG 1151 AACTTTGACA GCGACAAGAA GTGGGGCTTC TGCCCGGACC AAGGATACAG 1201 TTTGTTCCTC GTGGCGGCGC ATGAGTTCGG CCACGCGCTG GGCTTAGATC 1251 ATTCCTCAGT GCCGGAGGCG CTCATGTACC CTATGTACCG CTTCACTGAG 1301 GGGCCCCCCT TGCATAAGGA CGACGTGAAT GGCATCCGGC ACCTCTATGG 1351 TCCTCGCCCT GAACCTGAGC CACGGCCTCC AACCACCACC ACACCGCAGC 1401 CCACGGCTCC CCCGACGGTC TGCCCCACCG GACCCCCCAC TGTCCACCCC 1451 TCAGAGCGCC CCACAGCTGG CCCCACAGGT CCCCCCTCAG CTGGCCCCAC 1501 AGGTCCCCCC ACTGCTGGCC CTTCTACGGC CACTACTGTG CCTTTGAGTC 1551 CGGTGGACGA TGCCTGCAAC GTGAACATCT TCGACGCCAT CGCGGAGATT 1601 GGGAACCAGC TGTATTTGTT CAAGGATGGG AAGTACTGGC GATTCTCTGA 1651 GGGCAGGGGG AGCCGGCCGC AGGGCCCCTT CCTTATCGCC GACAAGTGGC 1701 CCGCGCTGCC CCGCAAGCTG GACTCGGTCT TTGAGGAGCC GCTCTCCAAG 1751 AAGCTTTTCT TCTTCTCTGG GCGCCAGGTG TGGGTGTACA CAGGCGCGTC 1801 GGTGCTGGGC CCGAGGCGTC TGGACAAGCT GGGCCTGGGA GCCGACGTGG 1851 CCCAGGTGAC CGGGGCCCTC CGGAGTGGCA GGGGGAAGAT GCTGCTGTTC 1901 AGCGGGCGGC GCCTCTGGAG GTTCGACGTG AAGGCGCAGA TGGTGGATCC 1951 CCGGAGCGCC AGCGAGGTGG ACCGGATGTT CCCCGGGGTG CCTTTGGACA 2001 CGCACGACGT CTTCCAGTAC CGAGAGAAAG CCTATTTCTG CCAGGACCGC 2051 TTCTACTGGC GCGTGAGTTC CCGGAGTGAG TTGAACCAGG TGGACCAAGT 2101 GGGCTACGTG ACCTATGACA TCCTGCAGTG CCCTGAGGAC TAGGGCTCCC 2151 GTCCTGCTTT GCAGTGCCAT GTAAATCCCC ACTGGGACCA ACCCTGGGGA 2201 AGGAGCCAGT TTGCCGGATA CAAACTGGTA TTCTGTTCTG GAGGAAAGGG 2251 AGGAGTGGAG GTGGGCTGGG CCCTCTCTTC TCACCTTTGT TTTTTGTTGG 2301 AGTGTTTCTA ATAAACTTGG ATTCTCTAAC CTTT TRANSLATE of: hum4cola.pr check: 644 from: 20 to: 2143 generated symbols 1 to: 708. LOCUS HUM4COLA 2334 bp ss-mRNA PRI 15-MAR-1990 DEFINITION Human type IV collagenase mRNA, complete cds. ACCESSION J05070 KEYWORDS collagenase; metalloprotease. SOURCE Human lung fibroblast cDNA to mRNA. . . . Hum4cola.pep Length: 708 February 15, 1991 10:58 Check: 184 .. 1 MSLWQPLVLV LLVLGCCFAA PRQRQSTLVL FPGDLRTNLT DRQLAEEYLY 51 RYGYTRVAEM RGESKSLGPA LLLLQKQLSL PETGELDSAT LKAMRTPRCG 101 VPDLGRFQTF EGDLKWHHHN ITYWIQNYSE DLPRAVIDDA FARAFALWSA 151 VTPLTFTRVY SRDADIVIQF GVAEHGDGYP FDGKDGLLAH AFPPGPGIQG 201 DAHFDDDELW SLGKGVVVPT RFGNADGAAC HFPFIFEGRS YSACTTDGRS 251 DGLPWCSTTA NYDTDDRFGF CPSERLYTRD GNADGKPCQF PFIFQGQSYS 301 ACTTDGRSDG YRWCATTANY DRDKLFGFCP TRADSTVMGG NSAGELCVFP 351 FTFLGKEYST CTSEGRGDGR LWCATTSNFD SDKKWGFCPD QGYSLFLVAA 401 HEFGHALGLD HSSVPEALMY PMYRFTEGPP LHKDDVNGIR HLYGPRPEPE 451 PRPPTTTTPQ PTAPPTVCPT GPPTVHPSER PTAGPTGPPS AGPTGPPTAG 501 PSTATTVPLS PVDDACNVNI FDAIAEIGNQ LYLFKDGKYW RFSEGRGSRP 551 QGPFLIADKW PALPRKLDSV FEEPLSKKLF FFSGRQVWVY TGASVLGPRR 601 LDKLGLGADV AQVTGALRSG RGKMLLFSGR RLWRFDVKAQ MVDPRSASEV 651 DRMFPGVPLD THDVFQYREK AYFCQDRFYW RVSSRSELNQ VDQVGYVTYD 701 ILQCPED*
P9323611@CCIT.ARIZONA.EDU (02/19/91)
Curious, I haven't been able to get a clear answer to a question I have had for almost a year now. I'm curious to know why researchers et. al. haven,t developed an in Vitro transcription system that could be utilized somewhat similar to the way the Polymerase Chain Reaction (PCR) is used. Instead of the crude extracts that are currently available on the market, can't the RNA polymerase from cells be purified and then used in a test tube containing: template DNA (containing the proper promoter sequence) RNA nucleotides ATP necessary ions this way a standardized method would be available -- in pre-prepared test tubes- for scientists to test specific transcription factors that are required for transcription of their particular gene. I know that different cells regulate their genes differently and by different mechanisms, but it seems to me that the basic necessary components of transcription should be available in a test tube. It seems like a standard system like this would supplement the current in vivo systems and would be relatively cheap. What is the limiting factor that is holding this technology back. Is it the purification of the RNA polymerase? Any information to these questions would be appreciated, John Pierpont, medical student University of Arizona