Remote access to ACNUC nucleotide and protein sequence databases at PBIL

被引：23

作者：

Gouy, Manolo ^{[1
]}

Delmotte, Stephane ^{[1
]}

机构：

[1] Univ Lyon 1, CNRS, UMR 5558, Lab Biometrie & Biol Evolut, F-69622 Villeurbanne, France

来源：

BIOCHIMIE | 2008年 / 90卷 / 04期

关键词：

ACNUC; bioinformatics; nucleotide sequence database; protein sequence database; database retrieval;

D O I：

10.1016/j.biochi.2007.07.003

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：

The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pole Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query-win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/ acnuc/acnuc.html). (C) 2007 Elsevier Masson SAS. All fights reserved.

引用

页码：555 / 562

页数：8

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