PupaSNP Finder protocols

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PupaSNP Finder specifications

Information


Unique identifier OMICS_24003
Name PupaSNP Finder
Alternative name PupaSNP
Interface Web user interface
Restrictions to use None
Input data A list of genes.
Output data A list of all the SNPs with possible phenotypic effect.
Computer skills Basic
Maintained No

Maintainer


This tool is not available anymore.

Publication for PupaSNP Finder

PupaSNP Finder in pipeline

2009
PMCID: 2762536
PMID: 19434427
DOI: 10.1007/s00439-009-0677-y

[…] is a companion tool to the snpper retrieval system and database that locates computationally predicted transcription factor-binding sites (riva and kohane ). both polymapr (freimuth et al. ) and pupasnp finder (conde et al. ) use computational methods to find possible exon splicing enhancer sites that can then be mapped to snp locations to find snps that potentially affect splicing. […]


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PupaSNP Finder in publications

 (11)
PMCID: 4141704
PMID: 25147926
DOI: 10.1371/journal.pone.0103872

[…] associations or known functional consequences (e.g. non-synonymous coding snps) if existent were preferred. information on snps was retrieved from databases ensmart (http://www.ensembl.org/), pupasnp , ucsc (http://genome.ucsc.edu), hapmap (www.hapmap.org), and dbsnp (http://www.ncbi.nlm.nih.gov/snp/)., three sets of family-trios, each trio comprising an ra patient ( = affected […]

PMCID: 3326031
PMID: 22529920
DOI: 10.1371/journal.pone.0034573

[…] regions, transcription factor binding sites, exonic splice enhancer sites, exonic splice silencer sites, triplet formation sites or intron-exon boundaries. pupasuite combines the functionality of pupasnp and pupasview in a unique and more integrated interface, and adds new modules to facilitate the selection of the optimal set of snps for a large-scale genotyping studies., we considered […]

PMCID: 3188581
PMID: 21998754
DOI: 10.1371/journal.pone.0026071

[…] protein kinase sequences were obtained from kinbase (http://kinase.com/kinbase/). sequence analysis of protein kinase mutations was done using data collected from different sources, including pupasnp , dbsnp database , online mendelian inheritance in man (omim) from national center for biotechnology information (ncbi) , , kinmutbase , , btkbase , human gene mutation database (hgmd) , , […]

PMCID: 2759519
PMID: 19834613
DOI: 10.1371/journal.pone.0007485

[…] have produced an unprecedented explosion of diverse data. a large amount of information about genetic modifications in protein kinase families has been accumulated in different sources, including pupasnp , dbsnp database , online mendelian inheritance in man (omim) from national center for biotechnology information (ncbi) , , kinmutbase , , btkbase , human gene mutation database (hgmd) , , […]

PMCID: 3153388
PMID: 19619005
DOI: 10.1359/jbmr.090729

[…] snps predicted to alter a transcription factor binding site and putative exon splice enhancers) with maf ≥ 1% were selected for genotyping. these putative functional snps were selected using either pupasnp (pupasuite.bioinfo.cipf.es/) or promolign (polly.wustl.edu/promolign/main.html).(,), in the second phase of the project (the validation sample), promising snp associations from the discovery […]


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PupaSNP Finder institution(s)
Bioinformatics Unit, Centro Nacional de Investigaciones Oncologicas (CNIO) Madrid, Spain; Hereditary Endocrine Cancer Group, Centro Nacional de Investigaciones Oncologicas (CNIO) Madrid, Spain
PupaSNP Finder funding source(s)
Supported by grant PI020919 from the Fondo de Investigaciones Sanitarias; by grant BIO2001-0068 from Ministerio de Ciencia y Tecnologia; a grant from Fundacio La Caixa and by the Spanish National Genotyping Centre (CeGen), funded by Genoma Espana, which is using this program for high-throughput SNP selection.

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