DetectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

ABSTRACT: Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, al

SUBMITTER: Ye C 

PROVIDER: S-EPMC4237412 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature