Bioinformatics Advance Access published March 22,.pdf

Bioinformatics Advance Access published March 22, 2007 Suresh B. Mudunuri and Hampapathalu A. Nagarajaram 2 (Wexler et al., 2004) and STRING (Parisi et al., 2003) have been designed to find tandem repeats of large size motifs as large as 2000 bases and hence large numbers of microsatellites go uniden- tified by these methods. Many of these programs do not generate alignments between imperfect microsatellites and their expected perfect counterparts and therefore require additional post- processing in order to study the mutational events in microsatel- lites. In view of these lacunae and to aid our systematic analysis of imperfect microsatellites, we developed a program called IMEx (Imperfect Microsatellite Extractor) with a number of discovery- friendly features. IMEx is fast, highly sensitive and is also flexible where user can set the limits for imperfection (thus can be used for both perfect and imperfect microsatellites). The output comprises of a list of microsatellites each of which with information such as its total imperfection content, point mutations, sequence alignment with its perfect counterpart, whether the locus lies in the coding or non-coding region along with corresponding known details. The IMEx program is available in two modes: as a stand-alone program and also in the form of a web-server. The stand-alone as well as web-server are available from the web-site 54/IMEX/ or .in/imex. 2 ALGORITHM We define a sequence at a given locus as a microsatellite if that sequence can be expressed as a tandem repeat of a motif of 1-6 bp size. The repeating motif at every iteration can harbor up to ‘k’ number of point mutations (substitutions or indels of nucleotides). For example, the sequence ATATGTAGAT is a tandem repeat of the motif “AT” with two substitutions A G and T G at third and fourth iterations respectively. IMEx algorithm uses this defini- tion and employs simple string searching algorithm with ‘sliding window’ appro