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

Authors: Sobreira, Tiago José P.; Durham, Alan M.; Gruber, Arthur

Source: Bioinformatics, Volume 22, Number 3, 1 February 2006 , pp. 361-362(2)

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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. 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@usp.br

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

Document Type: Research article

DOI: http://dx.doi.org/10.1093/bioinformatics/bti809

Publication date: 2006-02-01

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The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.