title: Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools.
abstract: BACKGROUND
  Common bean (Phaseolus vulgaris L.) is an important part of the human diet and serves as a source of natural products. Identification and understanding of genes in P. vulgaris is important for its improvement. Characterization of expressed sequence tags (ESTs) is one of the approaches in understanding the expressed genes. For the understanding of genes expression in P. vulgaris pod-tissue, research work of ESTs generation was initiated by constructing cDNA libraries using 5-day and 20-day old bean-pod-tissues. Altogether, 5972 cDNA clones were isolated to have ESTs. While processing ESTs, we found a transcript for calmodulin (CaM) gene. It is an important gene that encodes for a calcium-binding protein and known to express in all eukaryotic cells. Hence, this study was undertaken to analyse and annotate it.
  
  
  OBJECTIVE
  The objective of this study was to analyze and annotate P. vulgaris CaM (PvCaM) gene cDNA and its deduced protein (amino acids) sequence.
  
  
  METHODS
  Both strands of PvCaM cDNA clone were sequenced using M13 forward and reverse primer to elucidate the nucleotide sequence. The cDNA sequence and deduced protein sequence were analyzed and annotated using bioinformatics tools available online. The secondary structures and three-dimensional (3D) structure of PvCaM protein were predicted using the Phyre automatic fold recognition server.
  
  
  RESULTS
  Results showed that PvCaM cDNA is 818 bp in length. The cDNA analysis results showed that it contains an open reading frame that encodes for 149 amino acid residues. The deduced protein sequence analysis results showed the presence of conserved domains required for CaM function. The predicted secondary structures and 3D structure are analogous to the Solanum tuberosum CaM.
  
  
  CONCLUSIONS
  This study analyzed and annotated PvCaM cDNA and protein. However, in order to obtain a complete understanding of PvCaM protein, further study on its expression, structure and regulation is essential.
authors.affiliation: Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia.
authors.forename: Kassim
authors.initials: K
authors.lastname: Amelia
authors.affiliation: Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia.
authors.forename: Jasvin
authors.initials: J
authors.lastname: Singh
authors.affiliation: Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Research and Development, Novel Plants Sdn. Bhd., 27C Jln Petaling Utama 12, 7.5 Miles Old Klang Road, 46000 Petaling Jaya, Malaysia.
authors.forename: Farida Habib
authors.initials: FH
authors.lastname: Shah
authors.affiliation: Department of Molecular Biology, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka ; Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100, Kedah, Malaysia.
authors.forename: Subhash J
authors.initials: SJ
authors.lastname: Bhore
keywords: cDNA; expressed sequence tags; nutrition; phaseomics; proteins
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