Introduction to databases

Tuomas Hätinen

Topics

File Formats

Databases

- Primary structure: UniProt

- Tertiary structure: PDB

Database integration system

- Sequence retrieval system (eg SRS, Hands on session)

File formats

Fasta

FASTA format is very common. Can be hand constructed when in a hurry Straightforward way for storing multiple sequences – just concatenate

FASTA files Contents:

Line 1: > all identifiers and descriptors Remaining lines: sequence

>1NJR:A 32.1 KDA PROTEIN IN ADH3-RCA1 INTERGENIC REGIONXTGSLNRHSLLNGVKKXRIILCDTNEVVTNLWQESIPHAYIQNDKYLCIHHGHLQSLXDSXRKGDAIHHGHSYAIVSPGNSYGYLGGGFDKALYNYFGGKPFETWFRNQLGGRYHTVGSATVVDLQRCLEEKTIECRDGIRYIIHVPTVVAPSAPIFNPQNPLKTGFEPVFNAXWNALXHSPKDIDGLIIPGLCTGYAGVPPIISCKSXAFALRLYXAGDHISKELKNVLIXYYLQYPFEPFFPESCKIECQKLGIDIEXLKSFNVEKDAIELLIPRRILTLDL

Example of FASTA sequence for PDB 1njr. Note X are ’any’ amino acid.

SwissPROT, EMBL, TrEMBL, UniProt format

Each line begins with a 2

letter identifier

UniProt format closely

resembles EMBL format

except that considerably

more information about

physical and biochemical

properties is provided

SwissPROT format

Example of SwissProt entry. Line types are fully explained in:

http://au.expasy.org/sprot/userman.html#linetypes

SwissPROT format

Example of SwissProt entry. Line types are fully explained in:

http://au.expasy.org/sprot/userman.html#linetypes

Databases

Key concepts

Experimental database Contains experimental meassurements

E.g. EMBL, PDB

Derived database Derived from experimental databases

E.g. UniProtKB

Database stability Accession numbers

Non-redundancy Annotation

Nucleic sequence databases – experimental data

GenBank

DDBJ

EMBL

EBI

NCBI

CIB

*Submissions *Updates

EMBLNIG

NIH

*Submissions *Updates

*Submissions *Updates

EUROPEUSA

JAPAN

Raw Protein sequence databases

EBI

NCBI

EMBL

NIHGen Bank

DDBJ

EMBL

DNA sequences DBs Proteins seq DBs

Trans

Gen Pept

TrEMBL

SwissPROT

PIR-PSD

UniPROT

Trans

Entrez

Sub/Up

Sub/Up

Sub/Up

Sub/Up

SRS

UniProt

Universal Protein Resource Protein Sequence database UniProt Consortium

European Bioinformatics Institute

Swiss Institute of Bioinformatics

PIR Georgetown University

Mission

- Maintain high quality, stable, comprehensive, fully

classified and annotated protein sequence

knowledgebase, with extensive cross-references and

querying interfaces

Organization of UniProt databases

UniProt Archive (UniParc)

All available protein

sequences

UniProt Knowledgebase

(UniProtKB)

Annotated proteins

sequences

UniProt Reference Clusters

(UniRef)

Reduced redundancy for

faster searching

Database size comparison

Number of sequences

0 1 2 3 4 5 6 7 8 9

UniParc

UniProtKB

UniRef100

UniRef90

UniRef50

Millions

UniProtKB

Annontated entries UniParc =>UniProtKB UniProt/TrEMBL

Automated annotation

UniProt/SwissProt Manual annotation

SWISSPROT

Started as part of a Phd thesis, first version released in

1986. Now a collaboration between Swiss Institute of

Bioinformatics and EBI. Rich source for protein sequence data A well annotated source for sequences Largely non-redundant Updated daily, cross referenced with more than 30

different databases. Let us view a sample entry

TrEMBL

1996: TrEMBL (Translation of EMBL) released Computer-annotated entries derived from the translation

of all coding sequences in EMBL database except those

already in SWISS-PROT complement to Swiss-Prot and sequence

Sequences included to Swissprot by annotators

Errors in databases

Be aware of errors in the databases:

sequence errors:

- genome projects’ error rate is 1/10,000 nts;- ESTs’ error rate is 1/100nts.

annotation errors:

- Programs do not always give correct annotations.- SwissProt is a protein database curated and annotated manually

by biologists. - Manual curation doe

Errors in databases

Be aware of errors in the databases:

sequence errors:

- genome projects’ error rate is 1/10,000nts;- ESTs’ error rate is 1/100nts.

annotation errors:

- Automated computer programs do not always give correct annotations.

- SwissProt is a protein database curated and annotated manually by biologists.

- most reliable database, but is not up-to-date