Question: Prediction of the functional effect of nsSNPs
2
gravatar for sana.mystudies
3.2 years ago by
India
sana.mystudies60 wrote:

Dear All,

I am doing  few histone  protein's SNP analysis.

I have used SIFT  and  Polyphen for my initial analysis. now i would like predict its functional impact.

 can anyone please suggest me few tools or softwares for the prediction of the functional

effect of nsSNPs .thank you

ADD COMMENTlink modified 3.1 years ago by a.polo88100 • written 3.2 years ago by sana.mystudies60
4
gravatar for Pablo
3.2 years ago by
Pablo1.8k
Canada
Pablo1.8k wrote:

You can try SnpEff + SnpFit (dbNFSP)

http://snpeff.sourceforge.net/

 

NOTE: RamRs noted that the input data format is NOT from a sequencing experiment, but another format that lacks of the corresponding genomic coordinates. In such case, this recommendation is not appropriate for the analysis.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Pablo1.8k

SnpSift, you mean. Also, aren't these tools to use at VCF level? I think OP wants to go from AA mut to possible functional impact.

ADD REPLYlink written 3.2 years ago by Ram13k
1

Indeed. The question mentions "protein SNP analysis", so I'm assuming these are from sequencing data (otherwise it would be something like "protein polymorphism analysis"). May be sana can clarify a little bit more in the formats being used for the analysis...

 

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Pablo1.8k

"Protein polymorphism"? People use the term SNP without realizing they should be using mutation/variant - from my observation. I'm quite certain OP is referring a general variant/mutation and not a single nucleotide polymorphism.

ADD REPLYlink written 3.2 years ago by Ram13k
1

In Ensembl, we avoid using the term mutation unless the positions come from COSMIC and HGMD which are mutation databases. We use the term 'variants' instead...

ADD REPLYlink written 3.2 years ago by Denise - Open Targets4.1k
1

I agree. Calling AA variants "mutations" is more of my workplace convention than a general purpose terminology.

ADD REPLYlink written 3.2 years ago by Ram13k

OK, my bad then. I'll try to delete  / edit this answer.

 

ADD REPLYlink written 3.2 years ago by Pablo1.8k
1

All inputs help. In our field, out needs change everyday, no? I'm pretty sure OP will run into snpEff/SnpSift/VEP requirements soon enough :-)

ADD REPLYlink written 3.2 years ago by Ram13k
3
gravatar for a.polo88
3.1 years ago by
a.polo88100
Italy
a.polo88100 wrote:

this is a good question. there are many other tools to investigate the functional effect of the SNPs.

in first istance you can model the SNPs into your protein structure of interest simple using the homology modeling (using mutate_model that you can get from the website of modeller) once you obtain yuor structure with the point mutation yuo can perform three type of analysis using three bioinformatics tools :

DSSP you can assigne secondary structure both wildtype and to the variant protein and than you compare if there are a differences in the secondary structure(note that DSSP do not predict the secondary structure but only assigne a possibile structure)

HBPLUS you can use this tool to perform the analysis of the hydrogen bond to evaluate the pattern of hydrogen bond

NACCESS you can use this tools to evalute the accessible areas of the molecule

if you have any questions can contact me

 

ADD COMMENTlink written 3.1 years ago by a.polo88100

Thank you for the detailed reply..let me go through these..

ADD REPLYlink written 3.1 years ago by sana.mystudies60
3
gravatar for Denise - Open Targets
3.2 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.1k wrote:

The Perl script version of the Ensembl VEP has got a few plugins e.g. CADD, Condel and dbNSFP that can help you to predict the functional consequence of variants on Ensembl (and RefSeq) genes and transcripts.

ADD COMMENTlink written 3.2 years ago by Denise - Open Targets4.1k
2
gravatar for Ram
3.2 years ago by
Ram13k
New York
Ram13k wrote:

Have you tried PredictSNP? http://loschmidt.chemi.muni.cz/predictsnp/

ADD COMMENTlink written 3.2 years ago by Ram13k

No..Let me try...thanks

ADD REPLYlink written 3.2 years ago by sana.mystudies60
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