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galaxieEST: addressing EST identity through automated phylogenetic analysis
R Henrik Nilsson1, Balaji Rajashekar, Karl-Henrik Larsson
1Götenborg University, Botanical Institute, SE-405 30, Sweden. henrik.nilsson@botany.gu.se
BMC Bioinformatics
|July 9, 2004
Summary
This study introduces galaxieEST, a tool for identifying expressed sequence tags (ESTs) using automated phylogenetic analysis. It aids in accurately identifying gene families and orthology, especially for organisms lacking extensive genomic data.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Expressed sequence tag (EST) research relies on comprehensive sequence repositories, which are lacking for many organisms.
- Identifying paralogous genes and determining orthology is challenging due to high, incomplete sequence similarity.
- Phylogenetic analysis of query sequences aids in accurate identification when similarity searches are ambiguous.
Purpose of the Study:
- To develop an automated phylogenetic analysis tool to assist in the identification of expressed sequence tags (ESTs).
- To provide a method for accurate gene identification in organisms with limited genomic resources.
Main Methods:
- Developed galaxieEST, an open-source Perl-CGI script package.
- Utilized a series of BLAST runs to retrieve nucleotide and protein sequences.
- Performed neighbor-joining and parsimony phylogenetic analyses.
Main Results:
- galaxieEST integrates BLAST output, phylogenetic analysis results, and multiple alignments.
- The tool is available as an online web service for fungal EST identification.
- It can be downloaded for local installation and use with any organism group.
Conclusions:
- galaxieEST offers an integrative approach by considering sequence relatedness alongside similarity.
- This enhances the accuracy of EST origin and identity determination.
- It is particularly valuable when similarity searches yield ambiguous or incomplete matches, requiring further phylogenetic context.