CatSNP

Project Description

Single nucleotide polymorphisms (SNPs) and single base pair insertions and deletions (INDELs) play an important role in eukaryotic phenotypic changes. A change to a single base pair within a coding sequence or regulatory region can cause disease phenotypes with serious effects. With the recent development of high-throughput sequencing technologies and the subsequent increase in available full genome sequences, it is becoming clear that SNPs and INDELs also play an important role in prokaryotic phenotypic changes. A large number of tools are available to identify SNP/INDEL locations by comparative genomics and to provide information about a SNP/INDEL’s location within the genome and the resulting amino acid changes if it is located with a coding sequence. However, these tools do not provide information about the effect of the SNP/INDEL or link it to phenotypic changes within the cell.

The Cellular analysis tool for SNPs (CatSNP) is an Ondex plugin which filters Ondex networks to produce a sub-network that provides a systems-level view of the effects of SNPs and INDELs. In addition to providing information regarding the SNP/INDELs’ locations within the genome, CatSNP details the protein domains affected, and the Gene Ontology and KEGG annotations which are associated with these locations. Where detailed genomic information is available for a species, CatSNP also identifies SNPs/INDELs located within promoters, operators and terminators, together with annotation data of their associated gene.

CatSNP

Funding

The Ondex project is funded by the BBSRC:

  1. BB/F529038/1: Systems approaches to biological research training grant
  2. BB/F006063/1: From data to knowledge / the ONDEX System for integrating Life Sciences data sources