Genomic multiple sequence alignments: Refinement using a genetic algorithm

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Wang, Chunlin ^a   Lefkowitz, Elliot J ^a  

^a University of Alabama at Birmingham   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; EVOLUTIONARY RELATIONSHIPS; GENOMIC-SEQUENCE DATA; GENOTYPIC DIFFERENCES; LARGE GENOMIC SEQUENCES; MULTIPLE SEQUENCE ALIGNMENTS; PHENOTYPIC DIFFERENCES; REFINEMENT ALGORITHMS;

CLUSTERING ALGORITHMS; COMPUTER OPERATING SYSTEMS; GENES; OPTIMIZATION; TOOLS;

GENETIC ALGORITHMS;

NUCLEOTIDE DERIVATIVE;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOPOXVIRUS; PROCESS OPTIMIZATION; QUALITY CONTROL; SEQUENCE ALIGNMENT; VIRAL GENETICS; ALGORITHM; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; EVALUATION STUDY; GENETICS; GENOME; PROCEDURES; VALIDATION STUDY;

ORTHOPOXVIRUS;

ALGORITHMS; CLUSTER ANALYSIS; GENOME; MODELS, GENETIC; MODELS, MOLECULAR; ORTHOPOXVIRUS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 25444461357     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-200     Document Type: Article

References (33)

1. Ovcharenko I, Nobrega MA, Loots GG, Stubbs L: ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 2004, 32(Web Server issue):W280-6.
2. Brudno M, Steinkamp R, Morgenstern B: The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res 2004, 32(Web Server issue):W41-4.
3. Delcher AL, Phillippy A, Carlton J, Salzberg SL: Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30(11):2478-2483.
4. Baillie DL, Rose AM: WABA success: a tool for sequence comparison between large genomes. Genome Res 2000, 10(8):1071-1073.
5. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32(Web Server issue):W273-9.
6. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13(1):103-107.
7. Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13(1):97-102.
8. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13(4):721-731.
9. Gusfield D: Algorithm on Strings, Trees, and Sequences. Cambridge University Press; 1997:212.
10. Hirosawa M, Totoki Y, Hoshida M, Ishikawa M: Comprehensive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 1995, 11(1):13-18.
11. Nicholas HBJ, Ropelewski AJ, Deerfield DW: Strategies for multiple sequence alignment. Biotechniques 2002, 32(3):572-4, 576, 578 passim.
12. Notredame C, Holm L, Higgins DG: COFFEE: an objective function for multiple sequence alignments. Bioinformatics 1998, 14(5):407-422.
13. Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211-218.
14. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205-217.
15. Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443-453.
16. Holland JH: Adaptation in natural and artificial systems : an introductory analysis with applications to biology, control, and artificial intelligence. Ann Arbor, University of Michigan Press; 1975:viii, 183 p..
17. Notredame C, Higgins DG: SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res 1996, 24(8):1515-1524.
18. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.
19. Wang Y, Li KB: An adaptive and iterative algorithm for refining multiple sequence alignment. Comput Biol Chem 2004, 28(2):141-148.
20. Upton C, Hogg D, Perrin D, Boone M, Harris NL: Viral genome organizer: a system for analyzing complete viral genomes. Virus Res 2000, 70(1-2):55-64.
21. Thomsen R, Boomsma W: Multiple Sequence Alignment Using SAGA: Investigating the Effects of Operator Scheduling, Population Seeding, and Crossover Operators. 2004:113-122.
22. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611-1618.
23. LAM/MPI [http://charm.cs.uiuc.edu/]
24. Stoye J, Evers D, Meyer F: Rose: generating sequence families. Bioinformatics 1998, 14(2):157-163.
25. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Bench-marking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5(1):6.
26. Muller T, Rahmann S, Dandekar T, Wolf M: Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol 2004, 4(1):20.
27. Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22(2):160-174.
28. CHAOS/DIALIGN: [http://dialign.gobics.de/chaos-dialign-submission] [http://dialign.gobics.de/chaos-dialign-submission].
29. Ectromelia virus strain Naval - Sanger Institute [http://www.sanger.ac.uk/Projects/Ectromelia_virus/]
30. Gubser C, Smith GL: The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox. J Gen Virol 2002, 83(Pt 4):855-872.
31. Open Source Initiative [http://www.opensource.org/licenses/artistic-license.php]
32. FTP Site [ftp://ftp.genome.uab.edu/]
33. HPCL [http://ardra.hpcl.cis.uab.edu/]