publication . Article . Other literature type . 2009

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Cymon J. Cox; Thomas Hamelryck; Bartek Wilczyński; P. J. A. Cock; Brad Chapman; Tiago Antao; Iddo Friedberg;
Open Access
  • Published: 20 Mar 2009 Journal: Bioinformatics, volume 25, pages 1,422-1,423 (issn: 1367-4803, eissn: 1460-2059, Copyright policy)
  • Publisher: Oxford University Press (OUP)
  • Country: Portugal
Abstract
Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be direc...
Subjects
ACM Computing Classification System: GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
free text keywords: Biopython, Python, Applications Note, Sequence Analysis
Related Organizations
Funded by
FCT| SFRH/BD/30834/2006
Project
SFRH/BD/30834/2006
IMPROVED COMPUTATIONAL STRATEGIES TO DETECT SELECTION AND MOLECULAR ADAPTATION: NOVEL AND EFFICIENT POPULATION GENOMICS APPROACHES
  • Funder: Fundação para a Ciência e a Tecnologia, I.P. (FCT)
  • Project Code: SFRH/BD/30834/2006
  • Funding stream: SFRH | Doutoramento
23 references, page 1 of 2

Chapman, B, Chang, J. Biopython: Python tools for computational biology. ACM SIGBIO Newslett.. 2000; 20: 15-19

Chaudhuri, RR, Pallen, MJ. xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Res.. 2006; 34: D335-D337 [OpenAIRE] [PubMed]

Bateman, A. The Pfam protein families database. Nucleic Acids Res.. 2004; 32: D138-D141 [PubMed]

Beaumont, MA, Nichols, RA. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B. 1996; 263: 1619-1626

Benson, DA. GenBank. Nucleic Acids Res.. 2007; 35: D21-D25 [OpenAIRE] [PubMed]

Felsenstein, J. PHYLIP -phylogeny inference package (Version 3.2). Cladistics. 1989; 5: 164-166

Hamelryck, T, Manderick, B. PDB file parser and structure class implemented in Python. Bioinformatics. 2003; 19: 2308-2310 [OpenAIRE] [PubMed]

Hinsen, K. The molecular modeling toolkit: a new approach to molecular simulations. J. Comp. Chem.. 2000; 21: 79-85 [OpenAIRE]

Holland, RCG. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008; 24: 2096-2097 [OpenAIRE] [PubMed]

De Hoon, MJL. Open source clustering software. Bioinformatics. 2004; 20: 1453-1454 [PubMed]

Kauff, F. WASABI: an automated sequence processing system for multi-gene phylogenies. Syst. Biol.. 2007; 56: 523-531 [PubMed]

Kulikova, T. EMBL nucleotide sequence database in 2006. Nucleic Acids Res.. 2006; 35: D16-D20 [OpenAIRE] [PubMed]

Lavel, G, Excoffier, L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics. 2004; 20: 2485-2487 [OpenAIRE] [PubMed]

Maddison, DR. NEXUS: an extensible file format for systematic information. Syst. Biol.. 1997; 46: 590-621 [OpenAIRE] [PubMed]

Oliphant, TE. Guide to NumPy.. 2006

23 references, page 1 of 2
Abstract
Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be direc...
Subjects
ACM Computing Classification System: GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
free text keywords: Biopython, Python, Applications Note, Sequence Analysis
Related Organizations
Funded by
FCT| SFRH/BD/30834/2006
Project
SFRH/BD/30834/2006
IMPROVED COMPUTATIONAL STRATEGIES TO DETECT SELECTION AND MOLECULAR ADAPTATION: NOVEL AND EFFICIENT POPULATION GENOMICS APPROACHES
  • Funder: Fundação para a Ciência e a Tecnologia, I.P. (FCT)
  • Project Code: SFRH/BD/30834/2006
  • Funding stream: SFRH | Doutoramento
23 references, page 1 of 2

Chapman, B, Chang, J. Biopython: Python tools for computational biology. ACM SIGBIO Newslett.. 2000; 20: 15-19

Chaudhuri, RR, Pallen, MJ. xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Res.. 2006; 34: D335-D337 [OpenAIRE] [PubMed]

Bateman, A. The Pfam protein families database. Nucleic Acids Res.. 2004; 32: D138-D141 [PubMed]

Beaumont, MA, Nichols, RA. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B. 1996; 263: 1619-1626

Benson, DA. GenBank. Nucleic Acids Res.. 2007; 35: D21-D25 [OpenAIRE] [PubMed]

Felsenstein, J. PHYLIP -phylogeny inference package (Version 3.2). Cladistics. 1989; 5: 164-166

Hamelryck, T, Manderick, B. PDB file parser and structure class implemented in Python. Bioinformatics. 2003; 19: 2308-2310 [OpenAIRE] [PubMed]

Hinsen, K. The molecular modeling toolkit: a new approach to molecular simulations. J. Comp. Chem.. 2000; 21: 79-85 [OpenAIRE]

Holland, RCG. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008; 24: 2096-2097 [OpenAIRE] [PubMed]

De Hoon, MJL. Open source clustering software. Bioinformatics. 2004; 20: 1453-1454 [PubMed]

Kauff, F. WASABI: an automated sequence processing system for multi-gene phylogenies. Syst. Biol.. 2007; 56: 523-531 [PubMed]

Kulikova, T. EMBL nucleotide sequence database in 2006. Nucleic Acids Res.. 2006; 35: D16-D20 [OpenAIRE] [PubMed]

Lavel, G, Excoffier, L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics. 2004; 20: 2485-2487 [OpenAIRE] [PubMed]

Maddison, DR. NEXUS: an extensible file format for systematic information. Syst. Biol.. 1997; 46: 590-621 [OpenAIRE] [PubMed]

Oliphant, TE. Guide to NumPy.. 2006

23 references, page 1 of 2
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