Journal Article

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences

Matthew Horton, Natacha Bodenhausen and Joy Bergelson

in Bioinformatics

Volume 26, issue 4, pages 568-569
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp682
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences

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Motivation: We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, …) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

Availability: http://bergelson.uchicago.edu/software/marta

Contact: mhorton@uchicago.edu; jbergels@midway.uchicago.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1446 words. 

Subjects: Bioinformatics and Computational Biology

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