title: Linear predictive coding representation of correlated mutation for protein sequence alignment.
abstract: BACKGROUND
  Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that only represent conservation. There is no general way to represent correlated mutation and incorporate it with sequence alignment yet.
  
  
  METHODS
  We develop a novel method, CM profile, to represent correlated mutation as the spectral feature derived by using linear predictive coding where correlated mutations among different positions are represented by a fixed number of values. We combine CM profile with conventional sequence profile to improve alignment quality.
  
  
  RESULTS
  For distantly related protein pairs, using CM profile improves the profile-profile alignment with or without predicted secondary structure. Especially, at superfamily level, combining CM profile with sequence profile improves profile-profile alignment by 9.5% while predicted secondary structure does by 6.0%. More significantly, using both of them improves profile-profile alignment by 13.9%. We also exemplify the effectiveness of CM profile by demonstrating that the resulting alignment preserves share coevolution and contacts.
  
  
  CONCLUSIONS
  In this work, we introduce a novel method, CM profile, which represents correlated mutation information as paralleled form, and apply it to the protein sequence alignment problem. When combined with conventional sequence profile, CM profile improves alignment quality significantly better than predicted secondary structure information, which should be beneficial for target-template alignment in protein structure prediction. Because of the generality of CM profile, it can be used for other bioinformatics applications in the same way of using sequence profile.
authors.affiliation: Department of Bio and Brain Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon, 305-701, Korea.
authors.forename: Chan-seok
authors.initials: CS
authors.lastname: Jeong
authors.forename: Dongsup
authors.initials: D
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016014:Linear Models; D008958:Models, Molecular; D009154:Mutation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins
references.citation: Proteins. 2007;69 Suppl 8:38-56
references.pmid: 17894352
references.citation: Proteins. 2008 Aug 15;72(3):863-72
references.pmid: 18275083
references.citation: J Mol Biol. 1999 Nov 12;293(5):1221-39
references.pmid: 10547297
references.citation: Bioinformatics. 2008 Feb 1;24(3):333-40
references.pmid: 18057019
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92
references.pmid: 14681391
references.citation: J Mol Biol. 2000 Aug 18;301(3):679-89
references.pmid: 10966777
references.citation: Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):98-102
references.pmid: 8278414
references.citation: Science. 1999 Oct 8;286(5438):295-9
references.pmid: 10514373
references.citation: Nat Struct Biol. 2003 Jan;10(1):59-69
references.pmid: 12483203
references.citation: Proteins. 2007;69 Suppl 8:159-64
references.pmid: 17932918
references.citation: Proteins. 2002 Feb 15;46(3):330-9
references.pmid: 11835508
references.citation: Mol Biol Evol. 2000 Jan;17(1):164-78
references.pmid: 10666716
references.citation: J Mol Biol. 1995 Apr 7;247(4):536-40
references.pmid: 7723011
references.citation: BMC Bioinformatics. 2007 Dec 03;8:471
references.pmid: 18053160
references.citation: Bioinformatics. 2005 Apr 1;21(7):951-60
references.pmid: 15531603
references.citation: Bioinformatics. 2003 Apr 12;19(6):750-5
references.pmid: 12691987
references.citation: BMC Bioinformatics. 2006 Jul 25;7:357
references.pmid: 16869963
references.citation: J Mol Biol. 1999 Sep 17;292(2):195-202
references.pmid: 10493868
references.citation: Bioinformatics. 2000 Sep;16(9):776-85
references.pmid: 11108700
references.citation: Proteins. 2005 Jan 1;58(1):151-7
references.pmid: 15495137
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Proteins. 2008 May 1;71(2):950-9
references.pmid: 18004776
references.citation: Bioinformatics. 2004 Jul 10;20(10):1565-72
references.pmid: 14962924
references.citation: BMC Bioinformatics. 2007 Aug 28;8:314
references.pmid: 17725841
references.citation: Bioinformatics. 2009 May 1;25(9):1125-31
references.pmid: 19276150
references.citation: Nucleic Acids Res. 2004 Apr 30;32(8):2464-73
references.pmid: 15121903
references.citation: Proteins. 1994 Apr;18(4):309-17
references.pmid: 8208723
references.citation: Proteins. 2008 Aug;72(2):547-56
references.pmid: 18247410