300
Views
4
CrossRef citations to date
0
Altmetric
Original Articles

Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming

, &
Pages 3-13 | Received 29 Sep 2013, Accepted 22 May 2014, Published online: 18 Jun 2014

References

  • Pierri CL, Parisi G, Porcelli V. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. BBA-Protein Proteomics. 2010;1804:1695–1712. doi: 10.1016/j.bbapap.2010.04.008
  • Lambert C, Léonard N, De Bolle X, Depiereux E. ESyPred3D: prediction of proteins 3D structures. Bioinformatics. 2002;18:1250–1256. doi: 10.1093/bioinformatics/18.9.1250
  • Jani M, Azad RK. Information entropy based methods for genome comparison. ACM SIGBioinform Rec. 2013;3:2: 1–2:4.
  • Rosenberg MS. Sequence alignment: methods, models, concepts, and strategies. Berkeley: University of California Press; 2009.
  • Haque W, Aravind A, Reddy B. Pairwise sequence alignment algorithms: a survey. In: Proceedings of the 2009 conference on Information Science, Technology and Applications; ISTA ’09; Kuwait; New York: ACM. p. 96–103.
  • Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11:473–483. doi: 10.1093/bib/bbq015
  • Gibbs AJ, Mcintyre GA. The diagram, a method for comparing sequences. Eur J Biochem. 1970;16:1–11. doi: 10.1111/j.1432-1033.1970.tb01046.x
  • Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985;227:1435–1441. doi: 10.1126/science.2983426
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2
  • Pearson WR, Miller W. Dynamic programming algorithms for biological sequence comparison. Methods Enzymol. 1992;210:575–601. doi: 10.1016/0076-6879(92)10029-D
  • Pearson WR. Flexible sequence similarity searching with the FASTA3 program package. In: Misener S, Krawetz SA, editors. Bioinformatics methods and protocols. New York: Humana Press; 1999. p. 185–219.
  • Leslie C, Kuang R. Fast string kernels using inexact matching for protein sequences. J Mach Learn Res. 2004;5:1435–1455.
  • Zhao K, Chu X. G-BLASTN: accelerating nucleotide alignment by graphics processors. Bioinformatics. 2014. 10.1093/bioinformatics/btu047.
  • Di Tommaso P, Orobitg M, Guirado F, Cores F, Espinosa T, Notredame C. Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics. 2010;26:1903–1904. doi: 10.1093/bioinformatics/btq304
  • Harfe BD, Jinks-Robertson S. Removal of frameshift intermediates by mismatch repair proteins in Saccharomyces cerevisiae. Mol Cell Biol. 1999;19:4766–4773.
  • Farrell PM, Rosentein BJ, White TB, Accurso FJ, Castellani C, Cutting GR, Durie PR, Legrys VA, Massie J, Parad RB, Rock MJ, Campbell PW III. Guidelines for diagnosis of cystic fibrosis in newborns through older adults: cystic fibrosis foundation consensus report. J Pediatr. 2008;153(2):S4–S14.
  • Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci. 2010;107:12629–12633. doi: 10.1073/pnas.1007983107
  • Girdea M, Noe L, Kucherov G. Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms Mol Biol. 2010;5(1):1–15. doi: 10.1186/1748-7188-5-6
  • Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2010;2(12):1–5. doi: 10.1186/gm208
  • Yang X, Chockalingam SP, Aluru S. A survey of error-correction methods for next-generation sequencing. Brief Bioinform. 2013;14(1):56–66. doi: 10.1093/bib/bbs015
  • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341. doi: 10.1186/1471-2164-13-341
  • Connelly NG. Nomenclature of inorganic chemistry: IUPAC recommendations 2005. Cambridge: Royal Society of Chemistry Publishing; 2005.
  • Ripley L. Frameshift mutation: determinants of specificity. Annu Rev Genet. 1990;24:189–211. doi: 10.1146/annurev.ge.24.120190.001201
  • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147:195–197. doi: 10.1016/0022-2836(81)90087-5
  • Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982;162:705–708. doi: 10.1016/0022-2836(82)90398-9
  • Guan X, Uberbacher EC. Alignments of DNA and protein sequences containing frameshift errors. Comput Appl Biosci. 1996;12:31–40.
  • Huang X, Zhang J. Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci. 1996;12:497–506.
  • Lysholm F. Highly improved homopolymer aware nucleotide-protein alignments with 454 data. BMC Bioinform. 2012;13(1):1–13. doi: 10.1186/1471-2105-13-230
  • Chevillotte M, Einemvon J, Meier B, Lin F, Kestler HA, Mertens T. A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes. Antivir Res. 2010;85:318–327. doi: 10.1016/j.antiviral.2009.10.004
  • Fitch WM. Locating gaps in amino acid sequences to optimize the homology between two proteins. Biochem Genet. 1969;3:99–108. doi: 10.1007/BF00520346
  • Sankoff D, Cedergren RJ, Lapalme G. Frequency of insertion–deletion, transversion, and transition in the evolution of 5S ribosomal RNA. J Mol Evolut. 1976;7:133–149. doi: 10.1007/BF01732471
  • Altschul SF. Generalized affine gap costs for protein sequence alignment. Proteins. 1998;32:88–96. doi: 10.1002/(SICI)1097-0134(19980701)32:1<88::AID-PROT10>3.0.CO;2-J
  • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci. 1992;89:10915–10919. doi: 10.1073/pnas.89.22.10915
  • Dayhoff MO, Eck RV. Atlas of protein sequence and structure, 1967–68. Silver Spring, MD: National Biomedical Research Foundation; 1968.
  • Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM. An introduction to genetic analysis. 7th ed. New York: W.H. Freeman; 2000.
  • Michel D, Pavi I, Zimmermann A, Haupt E, Wunderlich K, Heuschmid M, Mertens T. The UL97 gene product of human cytomegalovirus is an early-late protein with a nuclear localization but is not a nucleoside kinase. J Virol. 1996;70:6340–6346.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.