Abstract
Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com.
Highlights
SSRs or microsatellites are the genetic loci where one or few bases are tandemly repeated for varying numbers of times
Tandem Repeat Occurrence Locator (TROLL) [8], uses a keyword tree adapted from bibliographic searching techniques and attempts to match the keywords exactly but it does not specify the positions of repeats
We describe a program called SSRscanner (Simple sequence repeat scanner) that uses dictionary approach to find simple sequence repeats of preselected motifs
Summary
Background: SSRs (simple sequence repeats) or microsatellites are the genetic loci where one or few bases are tandemly repeated for varying numbers of times. Available algorithms directly or indirectly detect tandem repeats. The drawbacks are high computational time required by the algorithm and their inability to predict the positions of SSRs in the genome. The program Tandem Repeats Finder [6] locates repeats with motifs of any size and type, including repeats with insertions and deletions.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
