Display options
Cite
Nord A, Carey K, Hornbeck P, et al. Splice-Aware Multiple Sequence Alignment of Protein Isoforms. ACM BCB. 2018;2018:200-210doi: 10.1145/3233547.3233592.
Nord, A., Carey, K., Hornbeck, P., & Wheeler, T. (2018). Splice-Aware Multiple Sequence Alignment of Protein Isoforms. ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2018200-210. https://doi.org/10.1145/3233547.3233592
Nord, Alex, et al. "Splice-Aware Multiple Sequence Alignment of Protein Isoforms." ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine vol. 2018 (2018): 200-210. doi: https://doi.org/10.1145/3233547.3233592
Nord A, Carey K, Hornbeck P, Wheeler T. Splice-Aware Multiple Sequence Alignment of Protein Isoforms. ACM BCB. 2018 Aug-Sep;2018:200-210. doi: 10.1145/3233547.3233592. PMID: 31080963; PMCID: PMC6508070.
Copy Download .nbib Format: NLM
Share it on

ACM BCB. 2018 Aug-Sep;2018:200-210. doi: 10.1145/3233547.3233592.

Splice-Aware Multiple Sequence Alignment of Protein Isoforms.

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine

Alex Nord, Kaitlin Carey, Peter Hornbeck, Travis Wheeler

Affiliations

  1. University of Montana Missoula, Montana, [email protected].
  2. University of Montana Missoula, Montana, [email protected].
  3. Cell Signaling Technology, Inc. Danvers, Massachusetts, [email protected].
  4. University of Montana Missoula, Montana, [email protected].

PMID: 31080963 PMCID: PMC6508070 DOI: 10.1145/3233547.3233592

Abstract

Multiple sequence alignment (MSA) is a classic problem in computational genomics. In typical use, MSA software is expected to align a collection of homologous genes, such as orthologs from multiple species or duplication-induced paralogs within a species. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need to create MSAs that more effectively accommodate isoforms. MSAs are traditionally constructed using scoring criteria that prefer alignments with occasional mismatches over alignments with long gaps. Alternatively spliced protein isoforms effectively contain exon-length insertions or deletions (indels) relative to each other, and demand an alternative approach. Some improvements can be achieved by making indel penalties much smaller, but this is merely a patchwork solution. In this work we present

Keywords: Multiple sequence alignment; alternative splicing; dual-coding exons; protein isoforms

References

  1. J Gen Virol. 2000 Jul;81(Pt 7):1675-86 - PubMed
  2. Genome Res. 2002 Apr;12(4):656-64 - PubMed
  3. Genome Res. 2002 Jun;12(6):996-1006 - PubMed
  4. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66 - PubMed
  5. J Biol Chem. 2003 Jan 17;278(3):1391-4 - PubMed
  6. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9 - PubMed
  7. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9 - PubMed
  8. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 - PubMed
  9. Biochem J. 2004 Jun 15;380(Pt 3):605-10 - PubMed
  10. BMC Bioinformatics. 2005 Feb 15;6:31 - PubMed
  11. Genome Res. 2006 Feb;16(2):190-6 - PubMed
  12. Curr Opin Struct Biol. 2006 Jun;16(3):368-73 - PubMed
  13. Bioinformatics. 2007 Jul 1;23(13):i559-68 - PubMed
  14. Nature. 2008 Nov 27;456(7221):470-6 - PubMed
  15. Nat Genet. 2008 Dec;40(12):1413-5 - PubMed
  16. Mol Cell Proteomics. 2009 Aug;8(8):1839-49 - PubMed
  17. J Virol. 2009 Oct;83(20):10719-36 - PubMed
  18. Nucleic Acids Res. 2010 Apr;38(7):2145-53 - PubMed
  19. Proteins. 1991;9(1):56-68 - PubMed
  20. Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5429-34 - PubMed
  21. Curr Opin Genet Dev. 2011 Feb;21(1):4-11 - PubMed
  22. Brief Bioinform. 2011 Sep;12(5):436-41 - PubMed
  23. Mol Syst Biol. 2011 Oct 11;7:539 - PubMed
  24. Nucleic Acids Res. 2012 Aug;40(15):7123-31 - PubMed
  25. Nucleic Acids Res. 2012 Nov 1;40(20):e161 - PubMed
  26. Science. 2012 Dec 21;338(6114):1593-9 - PubMed
  27. Genome Med. 2013 Feb 28;5(2):20 - PubMed
  28. Methods Mol Biol. 2014;1079:59-73 - PubMed
  29. Plant Cell. 2013 Oct;25(10):3640-56 - PubMed
  30. BMC Bioinformatics. 2014 Jun 14;15:189 - PubMed
  31. Nucleic Acids Res. 2015 Jan;43(Database issue):D512-20 - PubMed
  32. Blood. 2016 Jan 21;127(3):314-24 - PubMed
  33. Oncogene. 2016 Aug 18;35(33):4368-78 - PubMed
  34. Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761 - PubMed
  35. Mol Syst Biol. 2017 Dec 14;13(12):959 - PubMed
  36. Gene. 1988 Dec 15;73(1):237-44 - PubMed
  37. J Mol Biol. 1970 Mar;48(3):443-53 - PubMed

Publication Types

Grant support