title: RepEx: repeat extractor for biological sequences.
abstract: Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence(s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy.
authors.affiliation: Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.
authors.forename: M
authors.initials: M
authors.lastname: Gurusaran
authors.forename: Dheeraj
authors.initials: D
authors.lastname: Ravella
authors.forename: K
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D006801:Humans; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D020449:Repetitive Sequences, Amino Acid; D015203:Reproducibility of Results; D012984:Software; D020080:Tandem Repeat Sequences
keywords: Amino acid repeat sequence; Genome; Inverted repeat sequences; Palindromic repeat sequences; Repetitive sequences; Software