Overview

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 operates with a collection of entries of dbSNP mapped to the Golden Path genome assembly, as implemented in human section of Ensembl (Hubbard T. et al, 2005).

Requirements

Babelomics is designed as a web application so it can work on every OS: Windows, GNU/Linux and MacOS, all you need is a modern browser, i.e.: Firefox 3.x, Safari 4.x, Chrome 2.x, Opera 9.x or even IE 7.x. and IE 8.x. You only have to create an account to save you results, we give you a 1GB of disk space.

Current PupaSuite version uses:

  Ensembl version 56
  dbSNP 130
  HapMap rel.27
  Transfac Professional 8.3/Match 2.2
  Jaspar 3.0/Matscan 1.0
  ORegAnno
  Haploview v4.1     
  SNPeffect 3.0
  PAML 3.15
  GeneID

Last changes (Dec 2009):

  Rat and Mouse genomes are now included in PupaSuite
  JASPAR TFBS database has been included for searching SNPs in TFBSs
  OReagAnno TFBS database has been included for searching SNPs in TFBS
  New predictions: SNPs disrupting potential splices sites, SNPs in miRNAs and their targets, SNPs in Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS)
  HapMap has been updated to version 27
  Tagging is now done via the program Tagger implemented in Haploview, which has been updated to v4.1
  Output files can now be downloaded as text or Excel files 

Tool tutorials and WEB documentation

Advanced users

Web services

Work in progress

DAS server

Work in progress

Command Line Interface (CLI)

Work in progress