galaxieEST: addressing EST identity through automated phylogenetic analysis

BMC Bioinformatics
R Henrik NilssonBjörn M Ursing

Abstract

Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 1, 1997·Computer Applications in the Biosciences : CABIOS·R Mott
Sep 11, 2003·BMC Bioinformatics·Coral Del ValSandor Suhai
Feb 21, 2004·Bioinformatics·R Henrik NilssonBjörn M Ursing

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Citations

Jan 17, 2009·Source Code for Biology and Medicine·R Henrik NilssonNils Hallenberg

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Software Mentioned

Apache
Apache httpd Linux
MySQL
Clustal W
DBI Perl - MySQL
galaxieEST
BLASTn
Linux
Gene2EST
Genome

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