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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 REGION
XTGSLNRHSLLNGVKKXRIILCDTNEVVTNLWQESIPHAYIQNDKYLCIHHGHLQSLXDS
XRKGDAIHHGHSYAIVSPGNSYGYLGGGFDKALYNYFGGKPFETWFRNQLGGRYHTVGSA
TVVDLQRCLEEKTIECRDGIRYIIHVPTVVAPSAPIFNPQNPLKTGFEPVFNAXWNALXH
SPKDIDGLIIPGLCTGYAGVPPIISCKSXAFALRLYXAGDHISKELKNVLIXYYLQYPFE
PFFPESCKIECQKLGIDIEXLKSFNVEKDAIELLIPRRILTLDL
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/user
man.html#linet
ypes
SwissPROT format
Example of
SwissProt
entry. Line
types are fully
explained in:
http://au.expasy
.org/sprot/user
man.html#linet
ypes
Databases
Key concepts
 Experimental database
 Contains
 E.g.
experimental meassurements
EMBL, PDB
 Derived database
 Derived
 E.g.
from experimental databases
UniProtKB
 Database stability
 Accession
numbers
 Non-redundancy
 Annotation
Nucleic sequence databases – experimental data
NIH
NCBI
GenBank
*Submissions
*Updates
*Submissions
*Updates
EMBL
CIB
DDBJ
EBI
NIG
*Submissions
*Updates
EMBL
Raw Protein sequence databases
DNA sequences DBs
Sub/Up
Sub/Up
NCBI
NIH
Gen
Bank
Gen Pept
Trans
Entrez
PIR-PSD
SRS
DDBJ
EMBL
EBI
Sub/Up
Proteins seq DBs
EMBL
Trans
TrEMBL
Sub/Up
UniPROT
SwissPROT
UniProt
 Universal Protein Resource
 Protein Sequence database
 UniProt Consortium
 European
 Swiss
 PIR
Bioinformatics Institute
Institute of Bioinformatics
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
UniRef50
UniRef90
UniRef100
UniProtKB
UniParc
0
1
2
3
4
5
6
7
8
9
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