Hi everyone,
which other prediction tools (in addition to Provean) could be used to predict the Impact of indel mutations?
Thanks for your help! Andreas
If you want to infer a functional change from an indel, you need to map it onto the 3D structure. So the tools you need are BLAST to find a homolog and Rosetta, or MOE, or SwissModel, or some other tool to make a homology model. Then you need to read the literature and to learn as much as possible about the function(s). In other words, sorry, no short cut.
Tools like VeP and snpeff determine the effects of indels in known cases. Basically these are annotation tools.
If you would like to PREDICT the effect of indel mutations, my suggestion would be for you to try SIFT. There is also a webservice called the INDELZ (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-299)
These should help you!
Cheers
You can use SNPEff.
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
http://snpeff.sourceforge.net/
Typical usage :
Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
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