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

被引:29
作者
Pagni, M
Iseli, C
Junier, T
Falquet, L
Jongeneel, V
Bucher, P
机构
[1] Ludwig Inst Canc Res, Swiss Inst Bioinformat, CH-1066 Epalinges, Switzerland
[2] Ludwig Inst Canc Res, Swiss Inst Expt Canc Res, CH-1066 Epalinges, Switzerland
[3] Ludwig Inst Canc Res, Off Informat Technol, CH-1066 Epalinges, Switzerland
关键词
D O I
10.1093/nar/29.1.148
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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).
引用
收藏
页码:148 / 151
页数:4
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