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Bioinformatics Advance Access published online on January 29, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp067
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results

Jacques Lagnel 1,*, Costas S. Tsigenopoulos 1 and Ioannis Iliopoulos 2,*

1Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Heraklion 71003 and 2Division of Medical Sciences, University of Crete Medical School, Heraklion 71110, Crete, Greece

*To whom correspondence should be addressed. Jacques Lagnel, lagnel{at}her.hcmr.gr, Dr. Ioannis Iliopoulos, E-mail: ioannis{at}iti.gr


  Abstract

Summary: NOBLAST (New Options for BLAST) is an open source program that provides a new user friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria.

Availability: A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST.

Contact: lagnel{at}her.hcmr.gr

Contact: ioannis{at}iti.gr

Associate Editor: Prof. John Quackenbush

Received on October 7, 2008; revised on January 26, 2009; accepted on January 27, 2009

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