functional prediction SNP

[airtime]

Hi,

I have a list of SNP resulting from exome Re-Sequencing of tumor/normal human samples and GATK analyses. Now I searching Softwaretools for prediction (or better ) which analyse Mutation effect on Protein domain.

found:
1. SNP@DOMAIN (be no more available)
2. sift
3. ConDel
4. CanPredit
5. MutPred
6. polyphen and (2)
7. phastCons and GERP

All of this tools are not satisfactory for protein domain results. It is possible to combine one of the tools with databases like KEGG to get domains? Or is there another tool to handle this? Have someone further ideas to overcome this?

airtime

[sforsberg]

Hi airtime,

I´m not sure it is what you need but we are working on a tool to analyze impact of SNP on protein function. It takes two protein sequences as input, a reference sequence and a mutated sequence. It then assess the mutation impact based on 1) the magnitude of mutation-induced change in the local physicochemical characteristics of the protein, 2) secondary structure, 3) presence of motifs and domains, 4) the degree of conservation.

It is not yet finished but a beta version can be found on: https://github.com/simfor. The tool is implemented as a R-package.