Title

Authors

Affiliation

Agri-Bioinformatics Promotion Programme; Department of Agricultural Biotechnology; Assam Agricultural University; Jorhat-785013,Assam, India

Email

m17barooah@yahoo.co.in; *Corresponding author

Article Type

Hypothesis

Date

Received February 09, 2012; Accepted February 11, 2012; Published February 28, 2012

Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab. 

Keywords

Glutathione synthetase, Rhizobium etli CFN 42, Multiple Global Alignments, T-coffee, Degenerate Primers, Multiple Local Alignments, MEME, Primer3, MAST.

Citation

Sahu  et al. Bioinformation 8(4): 181-184 (2012)
 

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.