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

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 nu...

Descripción completa

Detalles Bibliográficos
Autores principales: Conde, Lucía, Vaquerizas, Juan M., Dopazo, Hernán, Arbiza, Leonardo, Reumers, Joke, Rousseau, Frederic, Schymkowitz, Joost, Dopazo, Joaquín
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538854/
https://www.ncbi.nlm.nih.gov/pubmed/16845085
http://dx.doi.org/10.1093/nar/gkl071
_version_ 1782129137388879872
author Conde, Lucía
Vaquerizas, Juan M.
Dopazo, Hernán
Arbiza, Leonardo
Reumers, Joke
Rousseau, Frederic
Schymkowitz, Joost
Dopazo, Joaquín
author_facet Conde, Lucía
Vaquerizas, Juan M.
Dopazo, Hernán
Arbiza, Leonardo
Reumers, Joke
Rousseau, Frederic
Schymkowitz, Joost
Dopazo, Joaquín
author_sort Conde, Lucía
collection PubMed
description 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 and through .
format Text
id pubmed-1538854
institution National Center for Biotechnology Information
language English
publishDate 2006
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-15388542006-08-18 PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes Conde, Lucía Vaquerizas, Juan M. Dopazo, Hernán Arbiza, Leonardo Reumers, Joke Rousseau, Frederic Schymkowitz, Joost Dopazo, Joaquín Nucleic Acids Res Article 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 and through . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538854/ /pubmed/16845085 http://dx.doi.org/10.1093/nar/gkl071 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Conde, Lucía
Vaquerizas, Juan M.
Dopazo, Hernán
Arbiza, Leonardo
Reumers, Joke
Rousseau, Frederic
Schymkowitz, Joost
Dopazo, Joaquín
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title_full PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title_fullStr PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title_full_unstemmed PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title_short PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
title_sort pupasuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538854/
https://www.ncbi.nlm.nih.gov/pubmed/16845085
http://dx.doi.org/10.1093/nar/gkl071
work_keys_str_mv AT condelucia pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT vaquerizasjuanm pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT dopazohernan pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT arbizaleonardo pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT reumersjoke pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT rousseaufrederic pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT schymkowitzjoost pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes
AT dopazojoaquin pupasuitefindingfunctionalsinglenucleotidepolymorphismsforlargescalegenotypingpurposes

Ejemplares similares