Dear all,
Now a days there are too many bioinformatic tools and sftwares freely available on the net like SIFT and Polyphen. These tools are able to predict the effect of specific varaiant on phenotype. My questions are:
1. why sometime these tools are unable to give results concerning specific variant.
2. to what level I can relay on these tools specially when they give different results?
We can not relay on the insilico evaluation of proteins prediction whether it benign or causing damage for a specific mutation e.g. (SNP's) specially when we consider the false negative possibilities. Other tools sould be considered such as mutation reporting among wild type, allele frequencies, novelty, relation to specific disease..etc. In addition, Further structural and functional studies required of this mutation to 100% correlate with available clinical presentation.
Thank you Mohammed, that is a good answer. But as you know some varaints are totally new which makes us question if the platform we are using detects a real varaints. I agree with you when it comes to population frequancy. relations with the disease, most of the time when you are looking at varaints you check of the function of the gene is correlated with the phenotype before considering it for analsysis. Functional studies definately are good but not when it come with point muatations.
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