Title

SSRscanner: a program for reporting distribution and exact location of simple sequence repeats

Authors

Tamanna Anwar¹ and Asad U Khan^1,2*

Affiliation

¹Distribution Information Sub-centre, ²Interdisciplinary Biotechnology Unit Aligarh Muslim University, Aligarh -202002, India *Corresponding author: Dr Asad U Khan, Lecturer, Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002 India.

E-mail*

huzzi99@hotmail.com; * Corresponding author

Phone

091-571-2723088

Fax

091-571-2721776

Article Type

Software

Date

received February 06 2006; Accepted February 12 2006; published online February 20, 2006

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.

Availability

This program has been written in PERL and is freely available for non-commercial users by request from the authors.

Keywords

scanner; SSR; repeats; script; microsatellite

Citation

Anwar & Khan, Bioinformation 1(3): 89-91 (2006)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.