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OJBTM
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.
ABSTRACT
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
by images.
Keywords: Energy
dot
plot, Structure dot plot, Minimum free energy, Dot-bracket
notation, MFE
Secondary structure, Centroid secondary structure.