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

Lucia Conde; Juan Vaquerizas; Hernán Dopazo; Leonardo Arbiza; Joke Reumers; Frederic Rousseau; Joost Schymkowitz; Joaquin Dopazo

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

Lucia Conde, Juan Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquin Dopazo

Research output: Contribution to journal › Article › peer-review

188 Citations (Scopus)

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.

Original language	English
Pages (from-to)	621-625
Number of pages	5
Journal	Nucleic Acids Research
Volume	34
Publication status	Published - 1 Jun 2006

Keywords

SNP

Access to Document

http://www.ncbi.nlm.nih.gov/pubmed/16845085

Cite this

@article{0829a5df782e465180dde454a00169e1,

title = "PupaSuite: ﬁnding functional single nucleotide polymorphisms for large-scale genotyping purposes.",

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.",

keywords = "SNP",

author = "Lucia Conde and Juan Vaquerizas and Hern{\'a}n Dopazo and Leonardo Arbiza and Joke Reumers and Frederic Rousseau and Joost Schymkowitz and Joaquin Dopazo",

year = "2006",

month = jun,

day = "1",

language = "English",

volume = "34",

pages = "621--625",

journal = "Nucleic Acids Res",

issn = "0305-1048",

publisher = "Oxford University Press",

}

PupaSuite: ﬁnding functional single nucleotide polymorphisms for large-scale genotyping purposes. / Conde, Lucia; Vaquerizas, Juan; Dopazo, Hernán; Arbiza, Leonardo; Reumers, Joke; Rousseau, Frederic; Schymkowitz, Joost; Dopazo, Joaquin.

In: Nucleic Acids Research, Vol. 34, 01.06.2006, p. 621-625.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - PupaSuite: ﬁnding functional single nucleotide polymorphisms for large-scale genotyping purposes.

AU - Conde, Lucia

AU - Vaquerizas, Juan

AU - Dopazo, Hernán

AU - Arbiza, Leonardo

AU - Reumers, Joke

AU - Rousseau, Frederic

AU - Schymkowitz, Joost

AU - Dopazo, Joaquin

PY - 2006/6/1

Y1 - 2006/6/1

N2 - 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.

AB - 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.

KW - SNP

M3 - Article

VL - 34

SP - 621

EP - 625

JO - Nucleic Acids Res

JF - Nucleic Acids Res

SN - 0305-1048

ER -

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

Abstract

Keywords

Access to Document

Fingerprint

Cite this