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PMID: 16845085 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.

Nucleic acids research ·Vol. 34 ·No. Web Server issue ·2006-07-01 ·Pages W621-5

Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J

Abstract

We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupasnp.org.

MeSH Terms
Algorithms Computer Graphics Databases, Nucleic Acid Evolution, Molecular Genotype Haplotypes Internet Linkage Disequilibrium Polymorphism, Single Nucleotide Software User-Computer Interface
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Conde Lucía
Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46013, Spain.
Vaquerizas Juan M
Dopazo Hernán
Arbiza Leonardo
Reumers Joke
Rousseau Frederic
Schymkowitz Joost
Dopazo Joaquín
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl071
Published
2006-07-01
Pages
W621-5
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1538854
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl071 PMC Full Text View journal details
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