Pupasuite 3

prioritization of SNPs in genotyping experiments based on functional properties


New features in Pupasuite 3.1:
  • Tools: Some tools have been upgraded and some fixes have been done
  • Performance improvements: Many libraries have been upgraded and some tools have been rewritten to speed up analysis
  • Bandwith usage: A more intelligent server communication has been developed, by doing this the bandwith has been reduce in almost 90%
  • Bug fixes: Some small bugs have been detected and fixed


PupaSuite is an interactive web-based SNP analysis tool that allows for the selection of relevant SNPs within a gene, based on different characteristics of the SNP itself, such as validation status, type, frequency/population data and putative functional properties (pathological SNPs, SNPs disrupting potential transcription factor binding sites, intron/exon boundaries...). Also, PupaSuite provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs (using the Haploview software)

PupaSuite was created to join PupaSNP & PupasView in a single, integrated suite, to improve their functionality and to implement 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 has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of SNP identifiers. Pupasuite is available at http://pupasuite.bioinfo.cipf.es

Homepage: http://pupasuite.bioinfo.cipf.es