Rabin-karp algorithm based microsatellite searching in whole-genome

Microsatellites (Simple Sequence Repeat) are abundant throughout genome sequences. The basic building block of a microsatellite is a short sequence motif (sequence pattern of 1-6 base-pairs in DNA) repeated in tandem. They are known for development of molecular markers, which play an important role in genetic diversity. In molecular biology, their identification and analysis play an important role in genomic studies. During present investigation, a formula-derived motif database was developed containing almost all possible motif combinations for user-desired lengths. An efficient microsatellite search program, based on the Rabin-Karp string matching algorithm, was also developed which can detect different microsatellite motifs' frequency, as per the user's parameters.