Amino acid substitutions can have many consequences (on protein stability / activity / folding / splicing / ...). If you want to do complex analysis, I recommend you to use tools such as SNPEffect (http://snpeffect.switchlab.org) or HOPE (http://www.cmbi.ru.nl/hope).

You mentioned three individual applications for different purposes: I-Mutant (stability predictor), SIFT (activity predictor) and POLYPHEN (pathogenicity predictor). In my opinion, dependence on single tools is not the best strategy because inaccuracies of these tools are still quite high. I prefer to use metaservers, i.e.:

- Pathogenicity: PredictSNP (http://loschmidt.chemi.muni.cz/predictsnp), Meta-SNP (http://snps.biofold.org/meta-snp/), PON-P (http://bioinf.uta.fi/PON-P), CONDEL (http://bg.upf.edu/condel/home)

- Stability: iSTABLE (http://predictor.nchu.edu.tw/istable)

If you want to know more about the tools focused on prediction of activity / stability, I recommend you these reviews / performance evaluations

- Potapov, 2009: http://peds.oxfordjournals.org/content/22/9/553

- Thusberg, 2011: http://www.ncbi.nlm.nih.gov/pubmed/21412949

- Khan, 2010: http://www.ncbi.nlm.nih.gov/pubmed/20232415

Thank you

jaroslav

Thanks abhishek

FoldX can be a valuable complementary tool to the ones mentioned above...

PROVEAN seems to be a real improvement over SIFT. I had trouble getting CONDEL

to work, but it might have been my fault, I think I used a fragment FASTA and I will go back and try again.

Some software tools link is given below:

http://www.cdfd.org.in/HANSA/index.php?target=related

I would strongly advise you to use Sibyl, if the mutations are SNPs in coding regions, as it offers by far the best accuracy (96%) in all literature. http://bioinformatics.ua.pt/sibyl

Thanks everyone for valuable suggestions...

Sibyl is not responding or working...is there something wrong with their website?

Mutation detection:

Generally samples are considered positive if both forward and reverse strands exhibit the same change. For this sequence of both strands of samples should be done followed by alignment of the FASTA format with the reference sequence in Clustal W software. We have to take about 10 reads of reference and sample (ratio should be 1:1) It should be checked that the reads supporting the mutation are identical i.e. mapping at exactly the same position. Skilled interpretation of the results is required, particularly to detect or exclude heterozygous mutations. Errors may be due to sequencer or PCR error. For sequencer error, try different sequencer. For PCR errors, try another polymerase, or try different primer (for e.g. more near or far away from the mutation). Other softwares which are used to detect the severity of the mutations are I mutant (stability predictor), SIFT (activity predictor) (http://sift.jcvi.org/), Polyphene2 (pathogenicitypredictor)(http://genetics.bwh.harvard.edu/pph2),mutationT@ster (http://www.mutationtaster.org/) SNPeffect (http://snpeffect.switchlab.org), HOPE (http://www.cmbi.ru.nl/hope), Sibyl(http://bioinformatics.ua.pt/sibyl), PMut(http://mmb2.pcb.ub.es:8080/PMut/), PhD-SNP (http://snps.biofold.org/phd-snp/), HANSA (http://www.cdfd.org.in/HANSA/index.php?target=home) and Stability predictor: iSTABLE (http://predictor.nchu.edu.tw/istable).

Look for Poly Peak Parser from Yost lab of university of Utah...

which soft ware is used for the prediction of non frame shift deletion???

I agree with Jaroslav.

I agree with Bendl

Well, usually you should analyze the impact of SNPs on protein function, stability, and interaction. Each one can be assessed using various software. Task one: SIFT, POLYPHEN-2, PhD-SNP, PROVEAN, PANTHER, ETC

For task two you can use: I-mutant, SDM.

For task 3: project hope, and others.

Ofc these work only for SNPs in coding region (exons)

MutationTaster is the best, online, up-to-date easy and free Parth Sarthi Sen Gupta

Many important tools were already mentioned, In addition, I suggest PredictSNP.

Does not work with indels

Polyphen2 . Sift , Phd snps panther is best for predication

i think different software having their own advantages and disadvantages .so for best interpretation or analysis .cannot rely on single one.comparison of results from all available software give good output

Gosnps panther snps

You can try CADD, which combines several prediction tools.

Really good is also VarCards:

http://159.226.67.237/sun/varcards/welcome

which software can be used for the indels..Such as I have one inframe deletion how can I check the effect of that mutation on the protein.

thanks

check this one samtools mpileup

Use SNP nexus https://www.snp-nexus.org

Polyphen-2 site is not opening, what can i do to open that server i need to do mutation Prediction in polyphen-2

You also can try EASE -MM (https://sparks-lab.org/server/ease-mm/) and Dynamut (http://biosig.unimelb.edu.au/dynamut/prediction) web servers.

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

http://ncblab.nchu.edu.tw/iStable2/about.html

http://provean.jcvi.org/index.php

http://www.vls3d.com/index.php/links/bioinformatics/mutations

http://www.mutationtaster.org/ is also a good one

It depends on which virus you have focused...

Maybe a Genetic algorithm or Neural Network would help you.