title: An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region.
abstract: 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.
authors.affiliation: Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat- 785013,Assam, India.
authors.forename: Mousumi
authors.initials: M
authors.lastname: Sahu
authors.forename: Jagajjit
authors.initials: J
authors.lastname: Sahu
authors.forename: Smita
authors.initials: S
authors.lastname: Sahoo
authors.forename: Budheswar
authors.initials: B
authors.lastname: Dehury
authors.forename: Kishore
authors.initials: K
authors.lastname: Sarma
authors.forename: Ranjan
authors.initials: R
authors.lastname: Sarmah
authors.forename: Priyabrata
authors.initials: P
authors.lastname: Sen
authors.forename: Mahendra Kumar
authors.initials: MK
authors.lastname: Modi
authors.forename: Madhumita
authors.initials: M
authors.lastname: Barooah