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

• Published in: Bioinformatics Vol. 22; no. 3; pp. 361 - 362
• Main Authors: Sobreira, Tiago José P., Durham, Alan M., Gruber, Arthur
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.02.2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Artificial Intelligence; Biological and medical sciences; Databases, Genetic; DNA - classification; DNA - genetics; Documentation - methods; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Pattern Recognition, Automated - methods; Sequence Analysis, DNA - methods; Software; Tandem Repeat Sequences - genetics; User-Computer Interface; Visualization; Automation; Computer program; Repeated sequence; HTML language; Classification; Method; Tandemly repeated sequence; Bioinformatics; Scope note; Annotation; Quantitative analysis
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti809

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 Contact:argruber@usp.br Supplementary Information: Supplementary data are available at