JCoDA: A tool for detecting evolutionary selection

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Steinway, Steven N ^a   Dannenfelser, Ruth ^a   Laucius, Christopher D ^a   Hayes, James E ^b   Nayak, Sudhir ^a  

^a Department of Health and Exercise Science   (United States)

^b Weill Graduate School of Medical Sciences of Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY RELATIONSHIPS; EVOLUTIONARY SELECTION; GRAPHICAL INTERFACE; PHYLOGENETIC ANALYSIS; PHYLOGENETIC TREES; SACCHAROMYCES GENOME DATABASE; SEQUENCE INFORMATIONS; VISUALIZATION TOOLS;

BIOLOGY; DATA VISUALIZATION; GENES; MAXIMUM LIKELIHOOD ESTIMATION; TOOLS; VISUALIZATION;

SITE SELECTION;

NEMATODA; SACCHAROMYCES;

ARTICLE; CODON; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN DATABASE; SEQUENCE ALIGNMENT;

CODON; DATABASES, GENETIC; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENOMICS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 77952720889     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-284     Document Type: Article

References (30)

1. Pirovano W, Heringa J. Multiple sequence alignment. Methods in molecular biology (Clifton, NJ) 2008, 452:143-161.
2. 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 research 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
3. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology 2000, 302(1):205-217. 10.1006/jmbi.2000.4042, 10964570.
4. Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC. IDEA: Interactive Display for Evolutionary Analyses. BMC bioinformatics 2008, 9:524. 10.1186/1471-2105-9-524, 2655098, 19061522.
5. Gupta SK, Kececioglu JD, Schaffer AA. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol 1995, 2(3):459-472. 10.1089/cmb.1995.2.459, 8521275.
6. Lipman DJ, Altschul SF, Kececioglu JD. A tool for multiple sequence alignment. Proceedings of the National Academy of Sciences of the United States of America 1989, 86(12):4412-4415. 10.1073/pnas.86.12.4412, 287279, 2734293.
7. Sze SH, Lu Y, Yang Q. A polynomial time solvable formulation of multiple sequence alignment. J Comput Biol 2006, 13(2):309-319. 10.1089/cmb.2006.13.309, 16597242.
8. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution 2007, 24(8):1586-1591. 10.1093/molbev/msm088, 17483113.
9. Liu G, Uddin M, Islam M, Goodman M, Grossman LI, Romero R, Wildman DE. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences. Source code for biology and medicine 2007, 2:5. 10.1186/1751-0473-2-5, 2093931, 17877817.
10. Endo T, Ikeo K, Gojobori T. Large-scale search for genes on which positive selection may operate. Molecular biology and evolution 1996, 13(5):685-690.
11. Korber B. Computational Analysis of HIV Molecular Sequences. HIV Signature and Sequence Variation Analysis 2000, 55-72. Dordrecht, Netherlands: Kluwer Academic Publishers, Learn AGRaGH.
12. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular biology and evolution 1986, 3(5):418-426.
13. Liang H, Zhou W, Landweber LF. SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic acids research 2006, (34 Web Server):W382-384. 10.1093/nar/gkl272, 1538794, 16845032.
14. Rozas J, Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics (Oxford, England) 1999, 15(2):174-175. 10.1093/bioinformatics/15.2.174, 10089204.
15. Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic acids research 2006, (34 Web Server):W609-612. 10.1093/nar/gkl315, 1538804, 16845082.
16. Holland RC, Down TA, Pocock M, Prlic A, Huen D, James K, Foisy S, Drager A, Yates A, Heuer M, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics (Oxford, England) 2008, 24(18):2096-2097. 10.1093/bioinformatics/btn397, 2530884, 18689808.
17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
18. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
19. Schmid K, Yang Z. The trouble with sliding windows and the selective pressure in BRCA1. PLoS ONE 2008, 3(11):e3746. 10.1371/journal.pone.0003746, 2581807, 19015730.
20. Massingham T, Goldman N. Detecting amino acid sites under positive selection and purifying selection. Genetics 2005, 169(3):1753-1762. 10.1534/genetics.104.032144, 1449526, 15654091.
21. Sawyer SL, Wu LI, Emerman M, Malik HS. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(8):2832-2837. 10.1073/pnas.0409853102, 549489, 15689398.
22. Zanotto PM, Kallas EG, de Souza RF, Holmes EC. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 1999, 153(3):1077-1089. 1460812, 10545443.
23. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular biology and evolution 1998, 15(5):568-573.
24. Pan C, Kim J, Chen L, Wang Q, Lee C. The HIV positive selection mutation database. Nucleic acids research 2007, (35 Database):D371-375. 10.1093/nar/gkl855, 1669717, 17108357.
25. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS biology 2003, 1(2):E45. 10.1371/journal.pbio.0000045, 261899, 14624247.
26. Francis R, Maine E, Schedl T. Analysis of the multiple roles of gld-1 in germline development: interactions with the sex determination cascade and the glp-1 signaling pathway. Genetics 1995, 139(2):607-630. 1206369, 7713420.
27. Haag ES, Ackerman AD. Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes. Gene 2005, 349:35-42. 10.1016/j.gene.2004.12.051, 15780968.
28. Clifford R, Lee MH, Nayak S, Ohmachi M, Giorgini F, Schedl T. FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline. Development (Cambridge, England) 2000, 127(24):5265-5276.
29. Lee MH, Schedl T. Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development. Genes & development 2001, 15(18):2408-2420. 312783, 11562350, 10.1101/gad.915901.
30. Nayak S, Goree J, Schedl T. fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis. PLoS biology 2005, 3(1):e6. 10.1371/journal.pbio.0030006, 539060, 15630478.