Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes

Mathematical Biology & Bioinformatics. 2012;7(2):461-475.

doi: 10.17537/2012.7.461.

1. DNA Repair, Genetic Instability, and Cancer. Eds. Wei Q, Li L, Chen DJ. World Scientific, 2007. doi: 10.1142/6228
2. Watson JD, Levine M, Baker TA, Gann A, Bell SP. Molecular Biology of the Gene. Benjamin-Cummings Pub. Corp.; 2007.
3. Okamura K, Feuk L, Marquès-Bonet T, Navarro A, Scherer SW. Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics. 2006;88:690-697. doi: 10.1016/j.ygeno.2006.06.009
4. Raes J, Van de Peer Y. Functional divergence of proteins through frameshift mutations. Trends Genet. 2005;21:428-431. doi: 10.1016/j.tig.2005.05.013
5. Kramer EM, Su H-J, Wu C-C, Hu J-M. A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineageBMC. Evolutionary Biology. 2006;6:30.
6. States DJ, Botstein D. Molecular sequence accuracy and the analysis of protein coding regions. Proc. Natl. Acad. Sci., USA. 1991;88:5518-5522.
7. Pearson WR, Wood T, Zhang Z, Miller W. Comparison of DNA sequences with protein sequences. Genomics. 1997;46:24-36. doi: 10.1006/geno.1997.4995
8. Birney E, Thompson J, Gibson T. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucl. Acids Res. 1996;24:2730-2739. doi: 10.1093/nar/24.14.2730
9. Guan X, Uberbacher EC. Alignments of DNA and protein sequences containing frameshift errors. Comput. Appl. Biosci. 1996;12:31-40.
10. Antonov I, Borodovsky M. Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J. Bioinform Comput Biol. 2010 Jun;8(3):535-51. doi: 10.1142/S0219720010004847
11. Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl. 2009;5(4):458-477. doi: 10.1504/IJBRA.2009.027519
12. Fichant GA, Quentin Y. A frameshift error detection algorithm for DNA sequencing projects. Nucleic Acids Res. 1995;23:2900-2908. doi: 10.1093/nar/23.15.2900
13. Médigue C, Rose M, Viari A, Danchin A. Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence. Genome Res. 1999;9:1116-1127. doi: 10.1101/gr.9.11.1116
14. Schiex T, Gouzy J, Moisan A, Oliveira YD. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res. 2003;31:3738-3741. doi: 10.1093/nar/gkg610
15. Frenkel FE, Korotkov EV. Classification analysis of triplet periodicity in protein-coding regions of genes. Gene. 2008;421:52-60. doi: 10.1016/j.gene.2008.06.012
16. Frenkel FE, Korotkov EV. Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes. DNA Res. 2009;16:105-114. doi: 10.1093/dnares/dsp002
17. Korotkov EV, Korotkova MA. Study of the triplet periodicity phase shifts in genes. Journal of Integrative Bioinformatics. 2010;7:31-141.
18. Fickett JW. Predictive methods using nucleotide sequences. Methods Biochem Anal. 1998;39:231-245. doi: 10.1002/9780470110607.ch10
19. Staden R. Statistical and structural analysis of nucleotide sequences. Methods Mol Biol. 1994;25:69-77.
20. Baxevanis AD. Predictive methods using DNA sequences. Methods Biochem Anal. 2001;43:233-252. doi: 10.1002/0471223921.ch10
21. Gutiérrez G, Oliver JL, Marín A. On the origin of the periodicity of three in protein coding DNA sequences. J Theor Biol. 1994 Apr 21;167(4):413-414. doi: 10.1006/jtbi.1994.1080
22. Gao J, Qi Y, Cao Y, Tung W-W. Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences. Journal of Biomedicine and Biotechnology. 2005;2:139-146. doi: 10.1155/JBB.2005.139
23. Yin C, Yau SS. Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence. Journal of Theoretical Biology. 2007;247:687-694. doi: 10.1016/j.jtbi.2007.03.038
24. Eskesen ST, Eskesen FN, Kinghorn B, Ruvinsky A. Periodicity of DNA in exons. BMC Molecular Biology. 2004;5:12. doi: 10.1186/1471-2199-5-12
25. Bibb MJ, Findlay PR, Johnson MW. The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene. 1984 Oct;30(1-3):157-166. doi: 10.1016/0378-1119(84)90116-1
26. Konopka AK. Sequences and codes: fundamentals of biomolecular cryptology. In: Biocomputing: Informatics and genome projects. Smith D Ed. San Diego, CA: Academic Press, 1994:119-174.
27. Trifonov EN. Elucidating sequence codes: three codes for evolution. Ann NY Acad Sci. 1999;870:330-338. doi: 10.1111/j.1749-6632.1999.tb08894.x
28. Eigen M, Winkler-Oswatitsch R. Transfer-RNA: the early adaptor. Naturwissenschaften. 1981;68:217-228. doi: 10.1007/BF01047323
29. Zoltowski M. Is DNA Code Periodicity Only Due to CUF - Codons Usage Frequency? In: Conf Proc IEEE Eng Med Biol Soc. 2007;1:1383-1386. doi: 10.1109/IEMBS.2007.4352556
30. Antezana MA, Kreitman M. The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J Mol Evol. 1999 Jul;49(1):36-43. doi: 10.1007/PL00006532
31. Korotkov EV, Korotkova MA, Frenkel FE, Kudryashov NA. Information approach for search of periodicity of symbolical sequences. Molek. Biol. (Russian). 2003;37:372-386.
32. Suvorova YM, Rudenko VM, Korotkov EV. Detection change points of triplet periodicity of gene. Gene. 2012;491:58-64. doi: 10.1016/j.gene.2011.08.032
33. Strauss BS. Frameshift mutation, microsatellites and mismatch repair. Mutation Research. 1999;437:195-203. doi: 10.1016/S1383-5742(99)00066-6
34. Korotkova MA, Kudryashov NA, Korotkov EV. An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity. Genomics Proteomics Bioinformatics. 2011;9:158-170. doi: 10.1016/S1672-0229(11)60019-3