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Data

Data. Sequences and Other Stuff. Sequence Data. Nucleic Acid and Protein Sequences. Sources of Genetic Sequences User GCG supplied databases Flat File Oracle Relational Database NCBI supplied databases Other databases. Sequence Databases. Genbank EMBL DDBJ NCBI PIR Swiss-Prot

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  1. Data Sequences and Other Stuff

  2. Sequence Data

  3. Nucleic Acid and Protein Sequences • Sources of Genetic Sequences • User • GCG supplied databases • Flat File • Oracle Relational Database • NCBI supplied databases • Other databases

  4. Sequence Databases • Genbank • EMBL • DDBJ • NCBI • PIR • Swiss-Prot • Swiss-Prot TrEMBL

  5. Genbank • Primary nucleic acid sequence database • Maintained by NCBI • National Center for Biotechnology Information • http://www.ncbi.nlm.nih.gov • Current Release 122, 2/2001 • 11,720,120,326 bases • 10,896,781 sequences

  6. Species 1995 1996 1997 1998 1999 2000 2001 Increase(since 1995) Increase(12 months) all: 16109 23119 32880 43516 61952 87751 95168 490% 40.9% Viruses: 1845 2122 2678 2968 3573 4428 4857 163% 32.4% Bacteria: 2939 3847 6091 8711 14322 22758 24878 746% 53.3% Archaea: 162 235 385 555 1015 1709 1906 1076% 68.8% Eukaryota: 10366 15901 22596 29926 41420 56961 61571 493% 37.4% How Many Organisms Are In The Sequence Databases?(April 1, 2001)

  7. Other NCBI Databases • HTGS • EST • STS • GSS • RefSeq • Unigene • Genomic

  8. HTGS High Throughput Genomic Sequences • ‘Unfinished' DNA sequences generated by the high-throughput sequencing centers • Phase 0 • Single-few pass reads of a single clone (not contigs) • Phase 1 • Unfinished, may be unordered, unoriented contigs, with gaps • Phase 2 • Unfinished, ordered, oriented contigs, with or without gaps • Phase 3 • Primary division (Genbank) • Finished, no gaps (with or without annotations)

  9. EST • Expressed Sequence Tags • “Single-pass" cDNA sequences • Generally representative of the 3’ ends of cDNAs • More “full-length” ESTs now available

  10. STS • Sequence Tagged Sites • Sequence and mapping data • Short genomic landmark sequences

  11. GSS • Genome Survey Sequences • Similar to the EST division, except that its sequences are genomic in origin, rather than cDNA • Random “single pass read” genome survey sequences. • Cosmid/BAC/YAC end sequences • Exon trapped genomic sequences • alu PCR sequences

  12. RefSeq • NCBI Reference Sequence project • Provides reference sequence standards for the naturally occurring molecules from chromosomes to mRNAs to proteins • Stable reference point for: • mutation analysis • gene expression studies • polymorphism discovery

  13. RefSeq… • Curated RefSeq • transcripts and proteins • Genome Annotation • contigs, transcripts, and proteins • Complete Genomes • genomes, chromosomes, and proteins

  14. Unigene • Experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters • Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. • Includes EST and cDNA sequences • Includes human, rat, mouse, cow and zebrafish

  15. HomoloGene • Curated and calculated orthologs and homologs for genes represented in UniGene and LocusLink • Includes human, mouse, rat, zebrafish, cow and drosophila

  16. LocusLink • Provides a single query interface to curated sequence and descriptive information about genetic loci • Nomenclature • Aliases • Sequence accessions • Phenotypes • EC numbers • MIM numbers • UniGene clusters • Homology • Map locations • Web sites

  17. EMBL and DDBJ • European Molecular Biology Laboratory • Hinxton, UK • http://www.ebi.ac.uk/ • DNA Data Bank of Japan • Mishima, Japan • http://www.ddbj.nig.ac.jp/

  18. Coordination with Genbank • Prevents duplication • Genbank enters sequences from U.S. journals and researchers • EMBL handles European data • DDBJ handles Asian data • Data exchanged daily

  19. Sequence submissions • Sequences entered from journals • Sequences submitted by individual researchers • BankIt • NCBI WWW Site • Sequin • Multi-platform program

  20. Sequence Names • DO NOT rely on names to find particular sequences • Few conventions • Organism • Hum: Human • Mus: mouse • Eco: E. coli • Syn: synthetic

  21. Last Letter(s) • Sometimes gives useful information • cg: Complete genome • Viruses

  22. Other Letters • Specifies a particular sequence • vsvcg • Vesicular stomatitis virus (Indiana serotype) complete genome

  23. EMBL File Names • Ec: E. coli • Hs: Human

  24. Locus name • Names are short, fairly non-descriptive, and can change from one release to another • vsvcg • The complete sequence for the virus VSV • Most “mnemonic” names already taken • Genbank now using accession numbers as locus names

  25. Accession Numbers • Each sequence submitted to a database is assigned a unique primary accession number • Accession numbers do not change • If a sequence is merged with another, a new accession number is assigned, and the original number becomes a secondary accession number • Accession numbers may include version numbers • AO2428.2

  26. Accession Numbers • Using GCG to access sequences via their accession number • Data Library:Accession Number • Flatfile - vi:JO2428 • RDB - gcgnuc: JO2428

  27. The Sequence Record • Different for each database • Locus (Name) • Accession Number • Keywords • Description • Properties • References • The Sequence

  28. analyze% typedata ge:humcftrm !!NA_SEQUENCE 1.0 LOCUS HUMCFTRM 6129 bp mRNA PRI 15-DEC-1989 DEFINITION Human cystic fibrosis mRNA, encoding a presumed transmembrane conductance regulator (CFTR). ACCESSION M28668 NID g180331 KEYWORDS cystic fibrosis; transmembrane conductance regulator. SOURCE Human, cDNA to mRNA. ORGANISM Homo sapiens Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 6129) AUTHORS Riordan,J.R., Rommens,J.M., Kerem,B., Alon,N., Rozmahel,R., Grzelczak,Z., Zielenski,J., Lok,S., Plavsic,N., Chou,J.-L., Drumm,M.L., Iannuzzi,M.C., Collins,F.S. and Tsui,L.-C. TITLE Identification of the cystic fibrosis gene: Cloning and characterization of complementary DNA JOURNAL Science 245, 1066-1073 (1989) MEDLINE 89368940

  29. COMMENT A three base-pair deletion spanning positions 1654-1656 is observed in cDNAs from cystic fibrosis patients. FEATURES Location/Qualifiers source 1. .6129 /organism="Homo sapiens" /db_xref="taxon:9606" CDS 133. .4575 /note="cystic fibrosis transmembrane conductance regulator" /codon_start=1 /db_xref="PID:g180332" /translation="MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVD SADNLSEKLEREWDRELASKKNPKLINALRRCFFWRFMFYGIFLYLGEVTKAVQPLLL LNRFSKDIAILDDLLPLTIFDFIQLLLIVIGAIAVVAVLQPYIFVATVPVIVAFIMLR AYFLQTSQQLKQLESEGRSPIFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTAN WFLYLSTLRWFQMRIEMIFVIFFIAVTFISILTTGEGEGRVGIILTLAMNIMSTLQWA VNSSIDVDSLMRSVSRVFKFIDMPTEGKPTKSTKPYKNGQLSKVMIIENSHVKKDDIW PSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLN TEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVAD EVGLRSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDP VTYQIIRRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSL FRQAISPSDRVKLFPHRNSSKCKSKPQIAALKEETEEEVQDTRL" BASE COUNT 1886 a 1181 c 1330 g 1732 t ORIGIN

  30. HUMCFTRM Length: 6129 April 13, 1998 13:00 Type: N Check: 6781 .. 1 AATTGGAAGC AAATGACATC ACAGCAGGTC AGAGAAAAAG GGTTGAGCGG 51 CAGGCACCCA GAGTAGTAGG TCTTTGGCAT TAGGAGCTTG AGCCCAGACG 101 GCCCTAGCAG GGACCCCAGC GCCCGAGAGA CCATGCAGAG GTCGCCTCTG 151 GAAAAGGCCA GCGTTGTCTC CAAACTTTTT TTCAGCTGGA CCAGACCAAT 201 TTTGAGGAAA GGATACAGAC AGCGCCTGGA ATTGTCAGAC ATATACCAAA 251 TCCCTTCTGT TGATTCTGCT GACAATCTAT CTGAAAAATT GGAAAGAGAA 301 TGGGATAGAG AGCTGGCTTC AAAGAAAAAT CCTAAACTCA TTAATGCCCT 351 TCGGCGATGT TTTTTCTGGA GATTTATGTT CTATGGAATC TTTTTATATT 401 TAGGGGAAGT CACCAAAGCA GTACAGCCTC TCTTACTGGG AAGAATCATA 451 GCTTCCTATG ACCCGGATAA CAAGGAGGAA CGCTCTATCG CGATTTATCT

  31. analyze% typedata -ref GB_PR:HUMIFNRF1A !!NA_SEQUENCE 1.0 LOCUS HUMIFNRF1A 7721 bp DNA PRI 10-NOV-1992 DEFINITION Homo sapiens interferon regulatory factor 1 gene, complete cds. ACCESSION L05072 NID g184648 KEYWORDS interferon regulatory factor 1. SOURCE Homo sapiens Placenta DNA. ORGANISM Homo sapiens Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 7721) AUTHORS Cha,Y., Sims,S.H., Romine,M.F., Kaufmann,M. and Deisseroth,A.B. TITLE Human interferon regulatory factor 1: intron/exon organization JOURNAL DNA Cell Biol. 11, 605-611 (1992) MEDLINE 93000481

  32. FEATURES Location/Qualifiers source 1. .7721 /organism="Homo sapiens" /db_xref="taxon:9606" /tissue_type="Placenta" /map="5q23-q31" exon 1. .219 /gene="IRF1" /note="putative" /number=1 5'UTR join(1. .219,1279. .1287) /gene="IRF1" gene join(1. .219,1279. .1287) /gene="IRF1" intron 220. .1278 /gene="IRF1" /number=1 exon 1279. .1374 /gene="IRF1" /number=2 CDS join(1288. .1374,2738. .2837,3630. .3806,3916. .3965, 4073. .4202,4386. .4508,5040. .5089,6248. .6383,6670. .6794) /gene="IRF1" /codon_start=1 /product="interferon regulatory factor 1" /db_xref="PID:g184649" /translation="MPITRMRMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKH GWDINKDACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKG SSAVRVYRMLPPLTKNQRKERKSKSSRDAKSKAKRKSCGDSSPDTFSDGLSSSTLPDD HSSYTVPGYMQDLEVEQALTPALSPCAVSSTLPDWHIPVEVVPDSTSDLYNFQVSPMP STSEATTDEDEEGKLPEDIMKLLEQSEWQPTNVDGKGYLLNEPGVQPTSVYGDFSCKE EPEIDSPGGDIGLSLQRVFTDLKNMDATWLDSLLTPVRLPSIQAIPCAP"

  33. intron 1375. .2737 /gene="IRF1" /number=2 exon 2738. .2837 /gene="IRF1" /number=3 intron 2838. .3629 /gene="IRF1" /number=3 exon 3630. .3806 /gene="IRF1" /number=4 intron 3807. .3915 /gene="IRF1" /number=4 exon 3916. .3965 /gene="IRF1" /number=5 intron 3966. .4072 /gene="IRF1" /number=5 ... exon 5040. .5089 /gene="IRF1" /number=8 intron 5090. .6247 /gene="IRF1" /number=8 exon 6248. .6383 /gene="IRF1" /number=9 intron 6384. .6669 /gene="IRF1" /number=9 exon 6670. .7656 /gene="IRF1" /number=10 3'UTR 6795. .7656 BASE COUNT 1750 a 1946 c 2253 g 1772 t ORIGIN

  34. analyze% typedata -ref est:hum091226f !!NA_SEQUENCE 1.0 LOCUS HUM091226F 152 bp mRNA EST 02-APR-1996 DEFINITION Homo sapiens retinal fovea EST HFV091226 sequence. ACCESSION L48850 NID g1254959 KEYWORDS EST; expressed sequence tag. SOURCE Homo sapiens (clone: EST HFV091226) age normalized retinal foveae cDNA to mRNA. ORGANISM Homo sapiens Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (sites) AUTHORS Adams,M.D., Kerlavage,A.R., Fields,C. and Venter,J.C. TITLE 3,400 new expressed sequence tags identify diversity of transcripts in human brain JOURNAL Nature Genet. 4 (3), 256-267 (1993) MEDLINE 93364420 REFERENCE 2 (sites) AUTHORS Liew,C.C., Hwang,D.M., Fung,Y.W., Laurenssen,C., Cukerman,E., Tsui,S. and Lee,C.Y. TITLE A catalogue of genes in the cardiovascular system as identified by expressed sequence tags JOURNAL Proc. Natl. Acad. Sci. U.S.A. 91 (22), 10645-10649 (1994) MEDLINE 95024171 REFERENCE 3 (bases 1 to 152) AUTHORS Bernstein,S.L., Borst,D.E., Neuder,M.E. and Wong,P. TITLE Characterization of a human fovea cDNA library and regional differential gene expression in the human retina JOURNAL Genomics 32 (3), 301-308 (1996)

  35. FEATURES Location/Qualifiers source 1. .152 /organism="Homo sapiens" /note="Expressed sequence tags (first pass sequencing) from randomly selected bacteriophage clones (mRNA-cDNA) from human retinal fovea. The library is age normalized from ten sets of donor foveae 2-79 years old. /db_xref="taxon:9606" /clone="EST HFV091226" /dev_stage="age normalized" /tissue_type="retinal foveae" mRNA <1. .>152 /standard_name="EST HFV091226" BASE COUNT 31 a 42 c 41 g 36 t 2 others ORIGIN

  36. analyze% typedata -ref sts:humswx153 !!NA_SEQUENCE 1.0 LOCUS HUMSWX153 192 bp DNA STS 24-MAY-1993 DEFINITION Human chromosome X STS sWXD153; single read. ACCESSION L15212 NID g292645 KEYWORDS STS; primer; sequence tagged site. SOURCE Homo sapiens DNA. ORGANISM Homo sapiens Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 192) AUTHORS Kere,J., Nagaraja,R., Mumm,S.R., Ciccodicola,A., D'Urso,M. and Schlessinger,D. TITLE Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts JOURNAL Genomics 14, 241-248 (1992) MEDLINE 93052321

  37. COMMENT Submitted by: David Schlessinger, Center for Genetics in Medicine, Washington University School of Medicine, Box 8232 4566 Scott Avenue, St. Louis, MO 63110, USA e-mail: davids@wugenmail.wustl.edu Primer A: TAAAGGGATCGCCAAGGAC Primer B: CTTACTCATTTGCTGGATTCTC STS size: 85bp Template: 600 ng/100ul Primer: 40 pmoles/100ul dNTPs: 100 uM MgCl2: 1.5 mM KCl: 100 mM TrisHCl: 10 mM Taq Polymerase: 0.125 U NH4Cl: 5 mM pH: 8.6 Total Vol: 5 ul PCR Profile: Denaturation: 94 degrees C for 1.00 minute(s) Annealing: 55 degrees C for 2.00 minute(s) Polymerization: 72 degrees C for 2.00 minute(s) PCR Cycles: 35 Thermal Cycler: P-E.

  38. FEATURES Location/Qualifiers source 1. .192 /organism="Homo sapiens" /db_xref="taxon:9606" /map="Xq13-q24" STS 60. .144 /standard_name="sWXD153" primer_bind 60. .78 primer_bind complement(123. .144) BASE COUNT 72 a 26 c 60 g 29 t 5 others ORIGIN analyze%

  39. Swiss-Prot http://www.expasy.ch/sprot/ • Protein Database • University of Geneva • Arranged by protein function • Release 39.15 • March 19, 2001 • 94,152 entries • Provides annotated protein records

  40. Swiss-Prot Names • Protein_Species • Allows easier comparisons when studying evolutionary relationships • H1b_Human • Human histone 1b

  41. Swiss-Prot Names • Vgl*_* • Viral glycoproteins • VGLG_HRSVL • Viral GLycoprotein G • Human Respiratory Syncytial Virus Long strain

  42. analyze% typedata swp:H1b_Human !!AA_SEQUENCE 1.0 ID H1B_HUMAN STANDARD; PRT; 218 AA. AC P10412; DT 01-MAR-1989 (REL. 10, CREATED) DT 01-MAR-1989 (REL. 10, LAST SEQUENCE UPDATE) DT 01-JUN-1994 (REL. 29, LAST ANNOTATION UPDATE) DE HISTONE H1B (H1.4). GN H1F4. OS HOMO SAPIENS (HUMAN). OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA; OC EUTHERIA; PRIMATES. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 92009931. RA ALBIG W., KARDALINOU E., DRABENT B., ZIMMER A., DOENECKE D.; RL GENOMICS 10:940-948(1991). RN [2] RP SEQUENCE. RC TISSUE=SPLEEN; RX MEDLINE; 87057092. RA OHE Y., HAYASHI H., IWAI K.; RL J. BIOCHEM. 100:359-368(1986).

  43. CC -!- FUNCTION: HISTONES H1 ARE NECESSARY FOR THE CONDENSATION OF CC NUCLEOSOME CHAINS INTO HIGHER ORDER STRUCTURES. CC -!- SUBCELLULAR LOCATION: NUCLEAR. CC -!- THIS VARIANT ACCOUNTS FOR 60% OF HISTONE H1. DR EMBL; M60748; G184074; -. DR PIR; A24413; HSHU1B. DR PIR; C40335; C40335. DR HSSP; P08287; 1GHC. KW CHROMOSOMAL PROTEIN; NUCLEAR PROTEIN; DNA-BINDING; MULTIGENE FAMILY; KW ACETYLATION; METHYLATION. FT INIT_MET 0 0 FT MOD_RES 1 1 ACETYLATION. FT MOD_RES 25 25 METHYLATION (PARTIAL). FT DOMAIN 35 113 GLOBULAR. SQ SEQUENCE 218 AA; 21734 MW; 5A277FB0 CRC32;

  44. H1B_HUMAN Length: 218 April 13, 1998 13:19 Type: P Check: 2701 .. 1 SETAPAAPAA PAPAEKTPVK KKARKSAGAA KRKASGPPVS ELITKAVAAS 51 KERSGVSLAA LKKALAAAGY DVEKNNSRIK LGLKSLVSKG TLVQTKGTGA 101 SGSFKLNKKA ASGEAKPKAK KAGAAKAKKP AGAAKKPKKA TGAATPKKSA 151 KKTPKKAKKP AAAAGAKKAK SPKKAKAAKP KKAPKSPAKA KAVKPKAAKP 201 KTAKPKAAKP KKAAAKKK analyze%

  45. Swiss-Prot TrEMBL • Translation of all EMBL Nucleic Acid coding sequences not yet present in Swiss-Prot • Allows rapid availability without immediate annotation • Release 16.3 • March 30, 2001 • 436,896 entries

  46. TrEMBL Divisions • Everything in TrEMBL: spt • sp_bacteria • sp_fungi • sp_human • sp_invertebrate • sp_mammal • sp_mhc • sp_organelle • sp_phage • sp_plant • sp_rodent • sp_unclassified • sp_vertebrate

  47. Protein Identification Resource - PIR http://pir.georgetown.edu/ • National Biomedical Research Foundation • Georgetown University • Current Release 67.05 • March 23, 2001 • 219,178 Entries

  48. National Biomedical Research Foundation • Database begun over twenty years ago by Margaret O. Dayhoff • Originally published sequences in book form • Started with sequences derived from direct amino acid sequencing

  49. analyze% typedata -ref PIR1:HSHU1B !!AA_SEQUENCE 1.0 P1;HSHU1B - histone H1-4 - human N;Alternate names: histone H1.4; histone H1b C;Species: Homo sapiens (man) C;Date: 31-Dec-1988 #sequence_revision 12-Apr-1996 #text_change 05-Sep-1997 C;Accession: C40335; A24413 R;Albig, W.; Kardalinou, E.; Drabent, B.; Zimmer, A.; Doenecke, D. Genomics 10, 940-948, 1991 A;Title: Isolation and characterization of two human H1 histone genes within clusters of core histone genes. A;Reference number: A40335; MUID:92009931 A;Accession: C40335 A;Status: preliminary A;Molecule type: DNA A;Residues: 1-219 <ALB> A;Cross-references: GB:M60748; NID:g184073; PID:g184074 A;Experimental source: blood R;Ohe, Y.; Hayashi, H.; Iwai, K. J. Biochem. 100, 359-368, 1986 A;Title: Human spleen histone H1. Isolation and amino acid sequence of a main variant, H1b. A;Reference number: A24413; MUID:87057092 A;Accession: A24413 A;Molecule type: protein A;Residues: 2-219 <OHE> A;Experimental source: spleen

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