trEST, trGEN and Hits: access to databases of predicted protein sequences.

Details

Serval ID
serval:BIB_18767
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
trEST, trGEN and Hits: access to databases of predicted protein sequences.
Journal
Nucleic acids research
Author(s)
Pagni M., Iseli C., Junier T., Falquet L., Jongeneel V., Bucher P.
ISSN
1362-4962[electronic]
Publication state
Published
Issued date
2001
Volume
29
Number
1
Pages
148-51
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't - Publication Status: ppublish
Abstract
High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).
Keywords
Amino Acid Sequence, Animals, Databases, Factual, Expressed Sequence Tags, Humans, Information Services, Internet, Markov Chains, Molecular Sequence Data, Proteins, Sequence Alignment, Sequence Homology, Amino Acid
Pubmed
Web of science
Open Access
Yes
Create date
19/11/2007 9:40
Last modification date
20/08/2019 12:48
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