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Bioinformatics Advance Access published online on December 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti809
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 21, 2005
Revised November 30, 2005
Accepted November 30, 2005

Applications note

TRAP: automated classification, quantification, and annotation of tandemly repeated sequences

Tiago José P. Sobreira 1, Alan M. Durham 2, and Arthur Gruber 3 *

1 Depto. de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil; Present address: Instituto do Coração - USP, Av. Prof. Enéas de Carvalho Aguiar 44, Bloco 2, 10° andar, 05403-000, São Paulo SP, Brazil
2 Depto. de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
3 Depto. de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil

* To whom correspondence should be addressed.
Arthur Gruber, E-mail: argruber{at}usp.br


  Abstract

Summary: TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and Comma-Separated Values (CSV). TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

Availability: TRAP is available under the GNU General Public License at http://www.coccidia.icb.usp.br/trap/.

Supplementary information: http://www.coccidia.icb.usp.br/trap/.


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