SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Pang, Andy ^a   Smith, Andrew D ^c   Nuin, Paolo A S ^a   Tillier, Elisabeth R M ^a,b  

^a PRINCESS MARGARET HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT METHODS; EVOLUTIONARY RELATIONSHIPS; HORIZONTAL GENE TRANSFER; MONTE-CARLO SIMULATIONS; PHYLOGENETIC TREES; SEQUENCE ALIGNMENTS; SEQUENCE ANALYSIS; STATISTICAL MODELING;

AMINO ACIDS; COMPUTER SIMULATION; COMPUTER SOFTWARE; GENE TRANSFER; INTELLIGENT SYSTEMS; TESTING;

PROTEINS;

ALLELE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; GENE DELETION; GENE INSERTION; GENE TRANSFER; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; BIOLOGICAL MODEL; GENETIC SELECTION; MOLECULAR EVOLUTION; PHYLOGENY; PROCEDURES;

AMINO ACID SUBSTITUTION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; SOFTWARE DESIGN;

EID: 27644471132     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-236     Document Type: Article

References (18)

1. Qian B, Goldstein RA: Distribution of Indel lengths. Proteins 2001, 45:102-4.
2. Thorne JL, Kishino H, Felsenstein J: An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol 1991, 33:114-124.
3. Thorne JL, Kishino H, Felsenstein J: Inching toward reality: an improved likelihood model of sequence evolution. J Mol Evol 1999, 34:3-16.
4. Metzler D: Statistical alignment based on fragment insertion and deletion models. Bioinformatics 2003, 19:490-499.
5. Miklos I, Lunter GA, Holmes I: A Long Indel model for evolutionary sequence alignment. Mol Biol Evol 2004, 21:529-40.
6. Benner SA, Cohen MA, Gonnet GH: Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J Mol Biol 1993, 229:1065-82.
7. Chang MS, Benner SA: Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol 2004, 341:617-31.
8. Rambaut A, Grassly NC: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13:235-8.
9. Grassly NC, Adachi J, Rambaut A: PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13(5):559-60.
10. Stoye J, Evers D, Meyer F: Rose: generating sequence families. Bioinformatics 1998, 14:157-163.
11. Dayhoff MO, Schwartz RM, Orcutt BC: A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure Volume 5. Edited by: Dayhoff MO. National Biomedical Research Foundation; 1978:345-352.
12. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 1992, 8:275-282.
13. Yang Z: Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 1993, 10:1396-1401.
14. Kondrashov AS, Rogozin IB: Context of deletions and insertions in human coding sequences. Hum Mutat 2004, 23:177-85.
15. Ogurtsov A, Aleksey Y, Sunyaev S, Kondrashov AS: Indel-based evolutionary distance and mouse-human divergence. Genome Res 2004, 14:1610-6.
16. Denver D, Morris K, Lynch M, Thomas WK: High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. 2004, 430:679-82.
17. Felsenstein J: PHYLIP (phylogeny inference package) version 3.6.3. 2002 [Http://evolution.genetics.washington.edu/phylip.html]. Available via the web
18. Thorne JL: Models of protein sequence evolution and their applications. Curr Opin Genet Dev 2000, 10:602-605.