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Sahu M, Sahu J, Sahoo S, Dehury B, Sarma K, Sarmah R, Sen P, Modi MK, Barooah M. An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region. Bioinformation 2012; 8:181-4. [PMID: 22419837 PMCID: PMC3301998 DOI: 10.6026/97320630008181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 02/11/2012] [Indexed: 11/23/2022] Open
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.
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Affiliation(s)
- Mousumi Sahu
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Jagajjit Sahu
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Smita Sahoo
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Budheswar Dehury
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Kishore Sarma
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Ranjan Sarmah
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Priyabrata Sen
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Mahendra Kumar Modi
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
| | - Madhumita Barooah
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013,Assam, India
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