Cours-Licence4

Derreumaux

Description

Bioinformatique Licence L3: Lecture 4P. DerreumauxBanques et bases de données généralistesThe first issue of each year of Nucleic Acids Researchis devoted to articles on biological databases.http://nar.oupjournals.org/Why do we need electronic databases ? 1. Data explosion 2. Data distributionWhat is a database ?1. computerized storehouse of data (records)2. allows user-defined queries3. allows extraction of specified records4. allows adding, changing, removing, and merging of records 5. uses standardized formatsStructure of databases1. ‘Structural’ Aspects (Id, ref, organism, links to other banks, function, phylogeny)2. ‘Expression’ Aspects (coding seq, exons, promoters, 3D structure, motifs, domains)3. Diminution of redondancies, e.g., NR Protein4. Quality criteria vary: automatic or human controlStructure «classique» d’un gène codant une protéine5’ UTR3’ UTRCDSintron intronCAAT TATA AUG T AAUAAexon exon exonMais un gène « classique », cela n’existe pas…. GenBank database recordLOCUS AF350270_1 691 aa linear INV 09-APR-2001StartDEFINITION fibroin 2 [Dolomedes tenebrosus].Accession codeACCESSION AAK30599PID g13561992VERSION AAK30599.1 GI:13561992DBSOURCE locus AF350270 accession AF350270.1KEYWORDS .SOURCE Dolomedes tenebrosus.ORGANISM Dolomedes tenebrosusEukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Araneae;Identifiers Araneomorphae; Entelegynae; Lycosoidea; ...

Informations

• Publié par: Movong
• Nombre de lectures: 23
• Langue: English

Extrait

Bioinformatique Licence L3: Lecture 4

P. Derreumaux

Banques et bases de données généralistes

The first issue of each year ofNucleic Acids Research is devoted to articles on biological databases. http://nar.oupjournals.org/

Why do we need electronic databases ?

1.

2.

Data explosion

Data distribution

1.

2.

3.

4.

5.

What is a database ?

computerized storehouse of data (records)

allows user-defined queries

allows extraction of specified records

allows adding, changing,removing, and mergingof records

uses standardized formats

1.

2.

3.

4.

Structure of databases

‘Structural’ Aspects (Id, ref, organism, links to other banks, function, phylogeny)

‘Expression’ Aspects (coding seq, exons, promoters, 3D structure, motifs, domains)

Diminution of redondancies, e.g., NR Protein

Quality criteria vary: automatic or human control

Structure «classique» d’un gène codant une protéine

CAAT TATA

5’ UTR

CDS

intron intron

AUG T

exon exon exon

3’ UTR

AAUAA

Mais un gène « classique », cela n’existe pas….

Star

GenBank database record

Identifiers

LOCUS AF350270 1 691 aa linear INV 09-APR-2001 _ D A E C F C I E N S I S T I I O O N N           f A i A b K r 3 o 05 i 9 n 9  2 [Dolomedestenebrosus]. Accession code PID g13561992 VERSION AAK30599.1 GI:13561992 DBSOURCE locus AF350270 accession AF350270.1 KEYWORDS . SOURCE Dolomedes tenebrosus. ORGANISM Dolomedes tenebrosus Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Lycosoidea; Pisauridae; Dolomedes. REFERENCE 1 (residues 1 to 691) AUTHORS Gatesy,J., Hayashi,C., Motriuk,D., Woods,J. and Lewis,R. TITLE Extreme diversity, conservation, and convergence of spider silk fibroin sequences JOURNAL Science 291 (5513), 2603-2605 (2001) MEDLINE 21179804 COMMENT Method: conceptual translation supplied by author. FEATURES Location/Qualifiers source 1..691 /organism="Dolomedes tenebrosus" /db xref="taxon:156846" _ Protein <1..691 /product="fibroin 2" /name="fibroin" CDS 1..691 /coded by="AF350270.1:<1..2078" _ ORIGIN 1 ygqgsgagaa aaaaaaggag qsgsgpygas ylssttytts sqgagggvgg ygqgsgtgsa 61 aaaagaagag qggqggygqg agqgglggyg qgggagaaaa aaaaaggags gqggyggqgg // End of record

Qualifiers

How to search for database records ?

1. - - - - - - -

Identifiers unique string of letters and digits that often are interpretable in a meaningful way by humans in GenBank:LOCUS(e.g. SCU32124) in SwissProt:ENTRY NAME(YNT2_YEAST) canchange !!! *** OTHER IDENTIFIERS *** VERSION= extension increases after every change GIchange completely when seq. is altered= may

Identifier

Version

OLC

GenBank Record

USSCU49845 5028 bpND ALPN 21-JUN-1999 

DEFINITIONSaccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSIONU49845 GenInfo Identifi VERSIONU49845.1GI:1293613 er KEYWORDS. SOURCEbaker's yeast. ORGANISMSaccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. REFERENCE1 (bases 1 to 5028) AUTHORSTorpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLECloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae

How to search for database records ?

2.

-

-

-

-

Accession numbers

in GenBank: 1 letter + 5 digits (U12345) or 2 letters + 6 digits (AF123456)

in SwissProt: 1 letter + 5 digits (P04049)

stable,does not change

will get transferred to new record if records are merged

*** USE ACCESSION NO. FOR SEARCHES ***  

Identifier

ACCESSION

Version

GenBank Record

LOCUSSCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITIONSaccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSIONU49845 VERSIONU49845.1GI:1293613 GenInfo Identifier KEYWORDS. SOURCEbaker's yeast. ORGANISMSaccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. REFERENCE1 (bases 1 to 5028) AUTHORSTorpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLECloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae

Nucleic acid sequence databases