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Bioinformatics Advance Access originally published online on December 6, 2005
Bioinformatics 2006 22(3):361-362; 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

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

Tiago José P. Sobreira 1,{dagger}, Alan M. Durham 2 and Arthur Gruber 1,*

1Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo São Paulo SP, 05508-000, Brazil
2Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo São Paulo SP, 05508-000, Brazil

*To whom correspondence should be addressed.

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. 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/

Contact: argruber{at}usp.br

Supplementary Information: Supplementary data are available at http://www.coccidia.icb.usp.br/trap/

Received on November 21, 2005; revised on November 30, 2005; accepted on November 30, 2005

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