PupaSuite is a web tool for the selection of SNPs with potential phenotypic effect, oriented to help in the design of large-scale genotyping projects and to the characterization of new SNPs from next generation technologies. 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 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.

PupaSuite 2 can input lists of SNPs, genes, or chromosomal regions and produce lists of SNPs with their possible phenotypic effect. Moreover, it can also calculate haplotypes and estimate the possible functionality of the corresponding combinations of SNPs.

PupaSuite can also produce graphic interactive analyses of single genes. There, a filter allows displaying SNPs potentially causing different types (structural, regulatory, splicing, etc.) and degrees of alterations.

The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupasuite.org.


Head of the Department: Joaquin Dopazo
Project Manager: Ignacio Medina
Software Developer: Joaquin Tarraga, Jose Carbonell