proteome databases
TRANSCRIPT
S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician
Proteomics
2D-PAGE & Proteome Databases2D-PAGE & Proteome Databases
S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA
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2D-PAGE
Decreasing pI
Decreasing MW
2-DE Gel Images
Annotated image of Silver stained E.coli 2-DE sample
Proteome
Proteomics covers the study of the proteins expressed by a genome in a biological sample, such as an organism, an organ, an organelle, a biological fluid
Analyze protein sequences for domains and active sites, perform similarity and homology searches, or predict the three-dimensional structure or physico-chemical parameters.
Protein sequence, nucleotide sequence, pattern/profile, 2-DE, 3-D structure, PTM, genomic, and metabolic.
Databases Types
Protein sequence databases
SWISS-PROT an annotated universal sequence database,TrEMBL an automatically generated sequence database with repository character, which supplements SWISS-PROT. SWISS-PROT [http://www.expasy.org/sprot/]
a curated protein sequence database which provides a high level of annotation
Types of Annotations: Description of a protein's function, its domain structure, PTMs, conflicts between literature references and variants. It also provides a minimal level of redundancy, a high level of integration with other bio molecular databases, and an extensive external documentation. (Created in 1986:Main Host-ExPaSy)
SWISSPROT format
Description Section
Reference Section
Comments Section
Database Cross-Reference Section
Keyword Field
Feature’s Table
Sequence
Low quality annotations, No SWISSPROT, but trEMBL
Genome Sequencing Projects SWISS-PROTannotators, who screen literature and sequence databases
Increase in available raw sequence data
Automatically populate SWISS-PROT with data of lower quality standards.
TrEMBL (Translation of EMBL Nucleotide Sequence Database)
Computer-annotated entries in SWISS-PROT-like format. It is populated by protein sequences translated from the coding sequences (CDS) in EMBL and is a supplement to SWISS-PROT
Nucleotide sequence databases
EBI in Great Britain distributing EMBL Nucleotide Sequence Database, NCBI in the USA distributing GenBank™, and the NIG in Japan distributing DDBJ
Collaboration: EMBL, GenBank and DDBJ all contain the same information
(the nucleotide sequence database is in fact one single database distributed under three different names, and in three different formats)Their format is not unified, but they share the same organizational principles as described for SWISS-PROT, i.e. a header containing the name of the sequence, the species of origin, followed by the references, a feature table, and the sequence data. EST to find CDS of gene- dbEST, hosted by NCBI
PROSITE regular expression patterns and profilesPfam HMMsPRINTS fingerprints (groups of aligned, unweighted motifs)Blocks aligned weighted motifs or blocks
ProDom is an automatic compilation of homologous domains, derived by clustering of SWISS-PROT and TrEMBL.
Databases for protein families, domains and functional sites
Above 4 Dbs formed InterPro consortium and developed InterPro, an integrated documentation resource for protein families, domains and functional sites.
2-DE databases
Information on proteins identified on 2-DE and consist of two major components: image data and textual information.
An image is the representation of a stained gel scanned optically. Apparent spots represent the position of focused protein forms and are linked to the textual information component of the database.
Textual information includes, Data on apparent pI and Mw of the spots, the name and description of the protein, the identification method, bibliographical references, and cross- references to SWISS-PROT and other databases.
SWISS-2DPAGE
The SWISS-2DPAGE database was created and is maintained at the SIB in collaboration with the University Hospital of Geneva.
In March 2000, it contained 26 reference maps from human, mouse, Saccharomyces cerevisiae, Escherichia coii and Dictyostellum Discoideum
It includes specific fields, such as
the type of master gel from which the protein spot has been identified, the list of gel images associated with the entry, as well as other 2-DE specific data, such as the mapping procedure, the spot identifier, the experimental pi and Mw, the peptide mass fingerprint and the amino-acid composition - if experimentally determined.
Post-translational modification databases
RESID a general database of protein structure modifications (http://www-nbrfgeorgetown.edu/pirwww/dbinfo/resid.html), maintained by the NBRF in the USA and the PIR group
The database contains descriptive, chemical, structural, and ibliographical information on 283 (Release 22.1, July 2000) types of modified amino-acid residues. GlycoSuiteDB (http://www.glycosuite.com) is an annotated database of glycan structures. The database is provided by Proteomesystems Ltd and contains information about most published O- and N-linked glycans.
O-GLYCBASE, a database of O-glycosylated proteins (http://www.cbs.dtu.dk/databases/OGLYCBASE/),
PhosphoBase, a database of phosphorylation sites in proteins and peptides (http://www.cbs.dtu.dk/databases/PhosphoBase/)
Both databases are maintained by the Center for Biological Sequence Analysis (CBS) in Denmark, which also provides prediction servers for both types of modifications (NetOGlyc and NetPhos).
Post-translational modification databases
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