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Bioinformatics Advance Access published online on February 19, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth119
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 22, 2003
Revised November 23, 2003
Accepted December 11, 2003

Article

Galaxie--CGI scripts for sequence identification through automated phylogenetic analysis

R. Henrik Nilsson 1*, Karl-Henrik Larsson 1, Björn M. Ursing 2

1 Botanical Institute, Göteborg University, Box 461, 405 30 Göteborg, Sweden
2 Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius v. 35, 171 77 Stockholm, Sweden

* To whom correspondence should be addressed. E-mail: henrik.nilsson{at}botany.gu.se.


  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 propriety of the outcome as basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was set up 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 Clustal W 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.botinst.gu.se/galaxiewelcome.html}}.


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