Polyphen-2 | Mutation Prediction & Verification Tool | Lecture 9 Part 2 By Dr. Muhammad Naveed

Mutational Analysis & Verification of the Mutations by using Polyphen-2
#Polyphen2 #MutationValidation #MutationPrediction

[@sherazahmad8274]

Great ....
Dear sir

[@tahiraaslam4365]

Good job👍

[@TasleemKhan-xu9zq]

Great sir thanks alot...

[@samannazeer227]

Great video.I've a question, how can we find dbSNP identifier for a protein?

[@scunnered5745]

In Polyphen2 there are the HumVAR prediction and the HumDIV prediction. Can you please tell me how these two predictions function and if they should both be used and how the contribute to the overall polyphen 2 variant effect predictor scoring?

[@applicwork276]

Assalamualaikum Sir your lacs are v informative thanks for your time
I have a query
Ic toll k results m mra hr dfa error a jta h what is the reason of that ?

[@tahiraghulam2733]

why we are not looking for HUmVar rather than HumDiv.? or when we look for each of them as they both are predicting different results.

[@bhavanisree2610]

Thank you sir! Good one

[@Prof.Dr.MuhammadNaveed]

Most welcome!

[@mairafatima1841]

SIR, PLZ MODpred ka bta dain... how to use it, as it it's website is not opening...

[@iqrach1193]

sir agr humny khud gene ki sequencing krwai ho to hum usy khud peptide seq main convert kr k wo protein seq yahan polyphen main or baqi jo protein verification k tools hain un sb main put krain gy ???????

[@Prof.Dr.MuhammadNaveed]

yes first translate by expasy or use blastX for your gene sequence to find mutations

[@madihahameed7663]

AOA very help full lecture thanks. i want to ask you if our results are possibly damaging then it is confirmed it is lead to cancer or how we interpret our results in research point of view

[@Prof.Dr.MuhammadNaveed]

means damaging

[@ahmadnaveed170]

Sir please tell me how can check Residues and DNA interaction and server or software can use for it.

[@Prof.Dr.MuhammadNaveed]

interaction with what? docking?

[@Anil-Behera]

Sir ...can we use polyphen software for Microbial protein sequence mutation analysis .......I think only for human protein analysis we can use this ..am I right ~ please reply me

[@Prof.Dr.MuhammadNaveed]

No dear we can use it for microbial as well

[@Anil-Behera]

@@Prof.Dr.MuhammadNaveed Thank You So Much Sir

[@madihahameed7663]

AOA please elloberate the difference between probable damage and possibly damage

[@Prof.Dr.MuhammadNaveed]

Probable refers to what is likely to be done ; possible refers to what can be done, to occur, or to be true

[@papridas8979]

Sir benign and damaged mutation me difference kya hai? Sensitivity and specificity are indicating severeity of mutation. Kindly reply sir.

[@Prof.Dr.MuhammadNaveed]

benign means no effect and damaged cause disease and yup

[@tahiraghulam2733]

sir, how can we get result in one go with list of SNPs. i have large number of SNPs of my gene of interest. Instesd of one by one is it possible to have result of all SNPs in one run.

[@Prof.Dr.MuhammadNaveed]

I always recommend to do one by one as whole difficult to characterize SNP

[@tahiraghulam2733]

@@Prof.Dr.MuhammadNaveed one more thing..how can i download spreadsheet from dbSNP in variation view for variation data

[@Prof.Dr.MuhammadNaveed]

@@tahiraghulam2733 you to to do one by one

[@areenakhan7969]

what substitution to select if residue change is termination?

[@Prof.Dr.MuhammadNaveed]

elaborate your query

[@sms861]

For eg if mutation results for a particular gene showing in gnoMAD is S302ter.
Which is termination codon, but polyphen 2 doesn't have option to search that.
Go for SIFT or other tools which allows termination and deletion codons

[@architsaxena8342]

Site of polyphen-2 is not reachable please help

[@Prof.Dr.MuhammadNaveed]

Sometime link down wait and try later on

[@asiyaijaz1359]

Sr yey mujy error dy rha h polyphen... k please enter either protein idenfier or dbSNP rsID, or a protein not both....I don't know how to overcome this

[@Prof.Dr.MuhammadNaveed]

means your mutation identification not correct

[@asiyaijaz1359]

@@Prof.Dr.MuhammadNaveed okay Sr thank u

[@hiramanzoor9436]

Can u guide how can we download polyphen software on windows

[@Prof.Dr.MuhammadNaveed]

better to use online

[@shershah5252]

How to identify novel mutation and verify novel mutation

[@Prof.Dr.MuhammadNaveed]

follow all this series

[@MsSADAFRANI]

sir can you please explain benign and damaged a little bit more. thankyou

[@Prof.Dr.MuhammadNaveed]

A mutation may be benign, a polymorphism, though present in some percentage of individuals, may be disease-causing and damaged means always disease-causing

[@MsSADAFRANI]

@@Prof.Dr.MuhammadNaveed so it is malignant basically.

[@Prof.Dr.MuhammadNaveed]

@@MsSADAFRANI YES

[@mohdsajad627]

Sir how to create a mutation at gene or protein levels

[@Prof.Dr.MuhammadNaveed]

why do you want to create? if you want to do this in silico then just delete that nucleotide which code the vital amino acid in expression

[@mohdsajad627]

@@Prof.Dr.MuhammadNaveedthank you so much sir. I want to do mutation at protein or gene level for alzheimer's disease. Because there are three enzymes, alpha, beta and gamma. But when mutation occurs in alpha or gamma, then beta forms beta peptides that result in the formation of disease. So i want to do mutation in beta and see what happens after that.

[@Prof.Dr.MuhammadNaveed]

@@mohdsajad627watch our video on mutation analysis. The method is the same for beta peptides as well.

[@niamatullahkhan67]

Sir how to predict a nonsense mutation using polyphene 2?

[@Prof.Dr.MuhammadNaveed]

same but depend upon its expression

[@niamatullahkhan67]

@@Prof.Dr.MuhammadNaveed Sir I'm asking about method.

[@hagarnofal2037]

Why not in English ?

[@Prof.Dr.MuhammadNaveed]

First series in native language next will be in English

[@viv7759]

English would have been preferred