BRM-Parser: A Tool for Comprehensive Analysis of BLAST and RepeatMasker Results

Article type: Research Article

Authors: Bajpai, Anjali | Sridhar, Settu | Reddy, Hemakumar M. | Jesudasan, Rachel A.

Affiliations: Center for Cellular and Molecular Biology, Hyderabad – 500007, India

Note: [] Corresponding author. E-mail: [email protected]

Abstract: BLAST and Repeat Masker Parser (BRM-Parser) is a service that provides users a unified platform for easy analysis of relatively large outputs of BLAST (Basic Local Alignment Search Tool) and RepeatMasker programs. BLAST Summary feature of BRM-Parser summarizes BLAST outputs, which can be filtered using user defined thresholds for hit length, percentage identity and E-value and can be sorted by query or subject coordinates and length of the hit. It also provides a tool that merges BLAST hits which satisfy user-defined criteria for hit length and gap between hits. The RepeatMasker Summary feature uses the RepeatMasker alignment as an input file and calculates the frequency and proportion of mutations in copies of repeat elements, as identified by the RepeatMasker. Both features can be run through a GUI or can be executed via command line using the standalone version.

Keywords: BLAST, RepeatMasker, repeats, parse, filter, merge, mutation

Journal: In Silico Biology, vol. 7, no. 4-5, pp. 399-403, 2007