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

Abstract

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. © The Author 2009. Published by Oxford University Press.