星系——通过自动系统发育分析进行序列识别的CGI脚本。

galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

作者信息

Nilsson R Henrik, Larsson Karl-Henrik, Ursing Björn M

机构信息

Botanical Institute, Goteborg University, Box 461, 405 30 Goteborg, Sweden.

出版信息

Bioinformatics. 2004 Jun 12;20(9):1447-52. doi: 10.1093/bioinformatics/bth119. Epub 2004 Feb 19.

DOI:10.1093/bioinformatics/bth119

PMID:14976034

Abstract

MOTIVATION

The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis.

RESULTS

Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable.

AVAILABILITY

A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

摘要

动机

像BLAST这样的相似性搜索普遍用于识别序列和物种，这隐含地假定参考数据库具有广泛的序列样本。但实际情况往往并非如此，这限制了作为序列识别基础的结果的正确性。系统发育推断在检索正确的系统发育关系以及相应的序列同一性方面优于相似性搜索，因此启动了一个项目，旨在设计一个可通过基于网络的自动系统发育分析进行序列识别的免费脚本包。