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Online Journal of Bioinformatics ©
Volume 15 (1): 35-48, 2014.
Prediction of secondary structure of human OPTC (Opticin) gene in region 1q32.1 of chromosome 1.
Akash kumar1, Mohd. Zakir Khawaja2*
1Department(s) of Bioinformatics, 2Biotechnology, Uttaranchal College of Science & Technology, Dehradun, India.
Kumar A, Khawaja Z., Prediction of secondary structure of human OPTC (Opticin( gene in region 1q32.1 of chromosome 1. Onl J Bioinform., 15(1): 35-48, 2014. Prediction of 2nd structure of region 1q32.1 of chromosome 1 of OPTC gene responsible for opticin protein generation is described. The mRNA sequence with accession number NM_014359.3 of the OPTC gene was retrieved in FASTA format, folded at 37șC and used to reveal an energy dot plot, minimum free energy and a suboptimal secondary structure at minimal free energy. The energy dot plot showed alternative base pairs in structure with free energies between -535.4 and -537.1 kcal/mol with a separation of < 12.0 kcal/mol from the lowest free energy structure. A mountain plot view showed that the centroid secondary structure had less loops and minimum free energy (MFE) compared with the secondary structure prediction which had the highest number of loops. The structures are illustrated in images.
Keywords: Energy dot plot, Structure dot plot, Minimum free energy, Dot-bracket notation, MFE Secondary structure, Centroid secondary structure.