@article {16845085,
	title = {PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes},
	journal = {Nucleic Acids Res},
	volume = {34},
	number = {Web Server issue},
	year = {2006},
	note = {<p>Conde, Lucia Vaquerizas, Juan M Dopazo, Hernan Arbiza, Leonardo Reumers, Joke Rousseau, Frederic Schymkowitz, Joost Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5.</p>},
	pages = {W621-5},
	abstract = {<p>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{\textquoteright}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.</p>},
	keywords = {Algorithms Computer Graphics Databases, Molecular Genotype Haplotypes Internet Linkage Disequilibrium *Polymorphism, Nucleic Acid Evolution, Single Nucleotide *Software User-Computer Interface},
	url = {http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621},
	author = {L. Conde and Vaquerizas, J. M. and H. Dopazo and Arbiza, L. and Reumers, J. and Rousseau, F. and Schymkowitz, J. and Dopazo, J.}
}
@article {15980522,
	title = {PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes},
	journal = {Nucleic Acids Res},
	volume = {33},
	number = {Web Server issue},
	year = {2005},
	note = {Conde, Lucia Vaquerizas, Juan M Ferrer-Costa, Carles de la Cruz, Xavier Orozco, Modesto Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5.},
	pages = {W501-5},
	abstract = {We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org.},
	keywords = {Computer Graphics Genes *Genetic Predisposition to Disease Genotype Internet Phenotype *Polymorphism, Single Nucleotide *Software User-Computer Interface},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=15980522},
	author = {L. Conde and Vaquerizas, J. M. and Ferrer-Costa, C. and de la Cruz, X. and Orozco, M. and Dopazo, J.}
}
