Mapping Variants to Protein Seqeunces

Question

[kautilya]

Hello,

1. I have a list of SNP variations(chr:pos:rsid if present:reference nucleotide:alternate nucleotide)
2. I want to map these variations to their corresponding position on the protein like Variation chr1:1234 maps to Amino Acid 33 on protein XYZ
3. Then output the protein sequence along with the mutated amino acid due to this variation.
4. I initially assumed there might be many tools to do this but upon looking I haven't been able to find any. I could also create my own solution but I need to reliably know which position each variant maps to in the protein.
5. I don't just have variants with known rsids, there are some variants which are novel.

Can anyone who has done something similar help me out on how to go about this?

Answer 1

[Emily]

You can use the Ensembl VEP. All you need are genome coordinates, and lots of formats can be used. The VEP will automatically give you the changed amino acid (if there is one), but to get the sequence of the mutated protein you'll need to use the standalone Perl script, along with a plugin. Here's some general info on plugins, and the plugin you'll need is ProteinSeqs.

Answer 2

[Alex Paciorkowski]

This may be similar to Snpeff - Annotating And Predicting The Effects Of Single Nucleotide Polymorphisms and also Tools to identify biologically relevant SNP calls from a vcf file

It sounds like you need to further annotate your variants. There are many such tools. Try the links above, and try these:

Ensembl's variant effect predictor: http://useast.ensembl.org/info/docs/tools/vep/index.html

Mutalyzer can also do what you seem to want: https://mutalyzer.nl/

Depending on where your list of variants came from, and the format of your data, you may find annotation tools like Annovar helpful