Question: How to choose good tools for identifying functional SNPs?
1
gravatar for arr234
18 months ago by
arr23420
arr23420 wrote:

If you look at the materials and methods of (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449402/) this paper, they have suggested using any three tools from each method (sequence homology-based methods, supervised learning methods, protein sequence and structure-based methods and consensus-based methods) to find the deleterious SNP. How do I choose the three best tools for each method?

snp • 893 views
ADD COMMENTlink modified 18 months ago by Kevin Blighe61k • written 18 months ago by arr23420
13
gravatar for Kevin Blighe
18 months ago by
Kevin Blighe61k
Kevin Blighe61k wrote:

Take your pick...

Sequence and evolutionary- / homology- / conservation-based methods (for missense predictions)

Protein sequence and structure-based methods (for missense predictions)

Supervised-learning methods (for missense predictions)

Splice predictions

Protein modelling (from amino acid sequence)

[uses various modelling algorithms and produces PDB files, which can be loaded into protein viewers like Jmol]

Non-coding (i.e. regulatory)

  • CADD (germline variants)
  • DANN (germline variants)
  • FATHMM-MKL (germline variants)
  • GWAVA (germline variants | somatic mutations)
  • Funseq2 (somatic mutations)
  • SurfR (rare variants | complex disease variants | all other variants)

Other


For further reading:

------------------------------------------------------------

I assure you that there are even more tools than these. These are categorised to the best of my and my colleague's knowledge.

Previous posting: A: pathogenicity predictors of cancer mutations

Kevin

ADD COMMENTlink modified 6 weeks ago • written 18 months ago by Kevin Blighe61k
3

Great list. Don't forget the Variant Effect Predictor (Coding/Protein, mostly), SnpEff (variety of fields), and DeepSea (Non-coding/Regulatory).

ADD REPLYlink written 18 months ago by jared.andrews076.1k

Thank you, Kevin Blighe. So now I can choose randomly any tool from each category in this list or should the choice be based on any criteria for best tools?

ADD REPLYlink written 18 months ago by arr23420

You could take a look through each and try to make your choices that way.

ADD REPLYlink modified 18 months ago • written 18 months ago by Kevin Blighe61k
1

Take a look at the material under 'further reading'. For example, in the UK, the clinical genetics regulatory body recommends certain tools over others.

ADD REPLYlink written 18 months ago by Kevin Blighe61k

what tools would you recommend to asses the effect of variants on ligand binding ?Schrodinger maestro seems good but it's a paid software.

ADD REPLYlink modified 18 months ago • written 18 months ago by Mehulsharma.25310

Sounds more like quantum chemistry ... ? Take a look at Spartan molecular modelling, although, you will require a powerful computer to accurately predict the effects. Could also look at the link that I posted under Protein modelling (from amino acid sequence)

ADD REPLYlink written 18 months ago by Kevin Blighe61k
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