Novel Approach to Analyzing MFE of Noncoding RNA Sequences.
Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.
Research Scholar, Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, Kerala, India.
Tina P
TP
George
Professor, Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, Kerala, India.
Tessamma
T
Thomas
digital signal processing; discrete Fourier transform; frequency spectrum; minimum free energy; multiple linear regression
J Cell Mol Med. 2002 Apr-Jun;6(2):279-303
12169214
RNA. 2005 Aug;11(8):1157-66
16043502
Nat Rev Genet. 2004 Jul;5(7):522-31
15211354
Annu Rev Biophys. 2008;37:197-214
18573079
J Mol Biol. 1997 Apr 18;267(5):1104-12
9150399
J Mol Biol. 2002 Jun 21;319(5):1059-66
12079347
Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):759-78
22991327
PLoS One. 2014 Nov 18;9(11):e113380
25405875
Bioessays. 2002 Dec;24(12):1164-77
12447981
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9
15665081
RNA. 2006 Mar;12(3):323-31
16495231
Science. 2002 May 17;296(5571):1260-3
12016301
Biopolymers. 1999 Feb;49(2):145-65
10070264
RNA. 2005 May;11(5):578-91
15840812
Cold Spring Harb Perspect Biol. 2011 Jun 01;3(6):null
20943759
Fold Des. 1998;3(2):69-78
9565751
Biochemistry. 1998 Oct 20;37(42):14719-35
9778347
Biopolymers. 1990 May-Jun;29(6-7):1105-19
1695107
Cell. 2004 Jan 23;116(2):281-97
14744438
Cell. 2014 Mar 27;157(1):77-94
24679528
Methods Mol Biol. 2008;453:3-31
18712296
Science. 1989 Apr 7;244(4900):48-52
2468181
J Mol Biol. 1999 Oct 22;293(2):271-81
10550208
Nucleic Acids Res. 2003 Dec 15;31(24):7280-301
14654704
BMC Res Notes. 2014 Jan 13;7:34
24418292
Nucleic Acids Res. 1981 Jan 10;9(1):133-48
6163133
Nature. 2004 Jul 8;430(6996):161-4
15241403
Nucleic Acids Res. 2001 Mar 1;29(5):1034-46
11222752
Nucleic Acids Res. 2003 May 1;31(9):e49
12711694
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Aug;82(2 Pt 1):021902
20866832
Nat Rev Genet. 2001 Dec;2(12):919-29
11733745
RNA. 2004 Aug;10(8):1178-90
15272118
J Mol Biol. 1999 May 21;288(5):911-40
10329189
Science. 2003 Mar 7;299(5612):1540
12624257
Nat Rev Genet. 2002 Oct;3(10):737-47
12360232
Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R17-29
16651366