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Bioinformatics Advance Access originally published online on November 5, 2004
Bioinformatics 2005 21(5):691-693; doi:10.1093/bioinformatics/bti075
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Published by Oxford University Press 2004.

ESTminer: a suite of programs for gene and allele identification

Rex T. Nelson *, David Grant and Randy C. Shoemaker *

USDA-ARS, CICGR Ames, IA, USA

*To whom correspondence should be addressed.

Summary: ESTminer is a collection of programs that use expressed sequence tag (EST) data from inbred genomes to identify unique genes within gene families. The algorithm utilizes Cap3 to perform an initial clustering of related EST sequences to produce a consensus sequence of a gene family. These consensus sequences are then used to collect all ESTs in the original EST library that are related using BLAST. A redundancy based criterion is applied to each EST to identify reliable unique gene-sequences. Using a highly inbred genome as a source of ESTs eliminates the necessity of computing covariance on each polymorphism to identify alleles of the same gene, thus making this algorithm more streamlined than other alternatives which must computationally attempt to distinguish genes from alleles.

Availability: The programs were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html

Contact: nelsonrt{at}iastate.edu

Supplementary information: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html


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