PDA: A pipeline to explore and estimate polymorphism in large DNA databases

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Casillas, Sònia ^a   Barbadilla, Antonio ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SUBSTITUTION; ARTICLE; AUTOMATION; CODON; COMPUTER PROGRAM; DNA POLYMORPHISM; GENE FUNCTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HISTOGRAM; INTERNET; POPULATION GENETICS; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

DATABASES, NUCLEIC ACID; INTERNET; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 3242876095     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh428     Document Type: Article

References (23)

1. Collins,F.S., Green,E.D., Guttmacher,A.E. and Guyer,M.S. (2003) A vision for the future of genomics research. Nature, 422, 835-847.
2. Rozas,J., Sanchez-DelBarrio,J.C., Messeguer,X. and Rozas,R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
3. Stein,L. (2002) Creating a bioinformatics nation. Nature, 417, 119-120.
4. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2004) GenBank: update. Nucleic Acids Res., 32, D23-D26.
5. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
6. Stein,L.D. (2001) Using Perl to facilitate biological analysis. In Ouellette,B.F.F. (ed.), Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Wiley-Liss, Inc., pp. 413-449.
7. Chenna,R., Sugawara,H., Koike,T., Lopez,R., Gibson,T.J., Higgins,D.G. and Thompson,J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
8. Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.
9. Nei,M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
10. Tajima,F. (1996) The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics, 143, 1457-1465.
11. Jukes,T.H. and Cantor,C.R. (1969) Mammalian protein metabolism. In Munro,H.N. (ed.), Evolution of Protein Molecules. Academic Press, New York, pp. 21-132.
12. Tajima,F. (1993) Mechanisms of molecular evolution. In Takahata,N. and Clark,A.G. (eds), Mesurement of DNA Polymorphism. Sinauer Associates Inc., Suderland, Massachusetts.
13. Tajima,F. (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460.
14. Tajima,F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
15. Nei,M. and Gojobori,T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426.
16. Sharp,P.M., Tuohy,T.M. and Mosurski,K.R. (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res., 14, 5125-5143.
17. Wright,F., (1990) The 'effective number of codons' used in a gene. Gene, 87, 23-29.
18. Sharp,P.M. and Li,W.H. (1987) The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281-1295.
19. Shields,D.C., Sharp,P.M., Higgins,D.G. and Wright,F. (1988) 'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol., 5, 704-716.
20. Lewontin,R.C. and Kojima,K. (1960) The evolutionary dynamics of complex polymorphisms. Evolution, 14, 458-472.
21. Lewontin,R.C. (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics, 49, 49-67.
22. Hill,W.G. and Robertson,A. (1968) Linkage disequilibrium in finite populations. Theor. Appl. Genet., 38, 226-231.
23. Kelly,J.K. (1997) A test of neutrality based on interlocus associations. Genetics, 146, 1197-1206.