PDA v.2: Improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Casillas, Sònia ^a   Barbadilla, Antonio ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; DATA ANALYSIS; DNA POLYMORPHISM; DNA SEQUENCE; DROSOPHILA; GENETIC HETEROGENEITY; GENETIC VARIABILITY; INFORMATION RETRIEVAL; INTERNET; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; QUALITY CONTROL; SCIENTIFIC LITERATURE; SPECIES DIVERSITY; ALGORITHM; ANIMAL; COMPUTER PROGRAM; GENETIC POLYMORPHISM; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; STANDARD;

ALGORITHMS; ANIMALS; DATABASES, NUCLEIC ACID; DROSOPHILA; INTERNET; POLYMORPHISM, GENETIC; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33747836261     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl080     Document Type: Article

References (7)

1. Casillas,S. and Barbadilla,A. (2004) PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res., 32, W166-W169.
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. Casillas,S., Petit,N. and Barbadilla,A. (2005) DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics, 21, ii26-ii30.
4. 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.
5. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
6. Edgar,R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
7. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.