- Communication -
| In Silico Biology 9, 0026 (2009); ©2009, Bioinformation Systems e.V. |
GEN-SNiP: an online tool to find polymorphisms in a genome
David B. Whyte1, Gopakumar Gopalakrishnan Nair2,*, Achuthsankar S. Nair2 and Oommen V. Oommen3
1 Argus Biosciences, 2033 Ralston Ave #84, Belmont, CA 94002, USA
2 Centre For Bioinformatics, University Of Kerala, Trivandrum 695581, India
3 Department Of Zoology, University Of Kerala, Trivandrum 695581, India
* Corresponding author
Email: gopakumar.cbi@gmail.com
Edited by E. Wingender; received April 03, 2009; revised May 07, 2009; accepted May 21, 2009; published June 01, 2009
Abstract
An online tool named GEN-SNiP that identifies variations in a set of test DNA sequences with respect to a standard reference sequence is developed and deployed successfully. The tool generates a list of substitutions, insertions and deletions for each test sequences, determined by the reference sequence. In the key batch mode feature, the tool allows multiple sequences to be compared and contrasted even when small insertions and deletions are present, with results sent to the user via email. Other distinguishing features of the tool are grouping of continuous deletions or insertions in the test sequence into a single entity for better output handling, displaying of the alignment of test and reference sequence and the input sequence. The tool has been reported as unique in recent literature.
Availability: GEN-SNiP is freely available at www.argusbio.com/sooryakiran/gensnip/gensnip.php.
Keywords: single nucleotide polymorphism (SNP), mitochondrial DNA (mtDNA), sequence analysis, genome, revised Cambridge reference sequence