PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA
Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (D...
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| Published in | Nucleic acids research Vol. 34; no. suppl-2; pp. W632 - W634 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.07.2006
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA v.2, incorporates substantial improvements, including new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface. PDA is a powerful tool to obtain and synthesize existing empirical evidence on genetic diversity in any species or species group. PDA v.2 is available on the web at http://pda.uab.es/. |
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| AbstractList | Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA v.2, incorporates substantial improvements, including new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface. PDA is a powerful tool to obtain and synthesize existing empirical evidence on genetic diversity in any species or species group. PDA v.2 is available on the web at http://pda.uab.es/. Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA v.2, incorporates substantial improvements, including new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface. PDA is a powerful tool to obtain and synthesize existing empirical evidence on genetic diversity in any species or species group. PDA v.2 is available on the web at . Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA v.2, incorporates substantial improvements, including new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface. PDA is a powerful tool to obtain and synthesize existing empirical evidence on genetic diversity in any species or species group. PDA v.2 is available on the web at . |
| Author | Casillas, Sònia Barbadilla, Antonio |
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| Copyright | Copyright Oxford University Press(England) 2006 The Author 2006. Published by Oxford University Press. All rights reserved 2006 |
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| Notes | http://www.nar.oupjournals.org/ istex:B611457B72D7E98DB7B6AF14628ECADDAC68F00B To whom correspondence should be addressed. Tel: +34 935 812 730; Fax: +34 935 812 387; Email: Antonio.Barbadilla@uab.es ark:/67375/HXZ-TXRRJ4GH-8 local:gkl080 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
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| References | 14668244 - Bioinformatics. 2003 Dec 12;19(18):2496-7 10964570 - J Mol Biol. 2000 Sep 8;302(1):205-17 16204116 - Bioinformatics. 2005 Sep 1;21 Suppl 2:ii26-30 15215372 - Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W166-9 12824352 - Nucleic Acids Res. 2003 Jul 1;31(13):3497-500 7984417 - Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 15034147 - Nucleic Acids Res. 2004;32(5):1792-7 |
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| SubjectTerms | Algorithms Animals Databases, Nucleic Acid DNA Drosophila Drosophila - genetics genetic polymorphism genetic variation Internet Internet resource new methods nucleotides Polymorphism, Genetic Quality Control Sequence Alignment - standards Sequence Analysis, DNA - methods Software - standards user interface User-Computer Interface world wide web |
| Title | PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA |
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