Is there a way to retrieve peptide motifs based on MAF/VEP output?

Question

[ddzhangzz]

Using the Ensembl's Variant Effect Predictor (VEP) program I evaluated the variants identified form GATK::MuTect2. The output looks like this:

Uploaded_variation     Location        Allele  Gene    Feature Feature_type    Consequence     cDNA_position   CDS_position    Protein_position        Amino_acids     Codons  Existing_variation      Extra
.       1:15710417      A       ENSMUSG00000092083      ENSMUST00000170146      Transcript      synonymous_variant      1512    1512    504     S       tcC/tcA -       IMPACT=LOW;STRAND=1
.       1:15710417      A       ENSMUSG00000092083      ENSMUST00000175681      Transcript      synonymous_variant      1832    1512    504     S       tcC/tcA -       IMPACT=LOW;STRAND=1
rs32076694      1:15833428      G       ENSMUSG00000025925      ENSMUST00000027057      Transcript      synonymous_variant      863     849     283     L       ttA/ttG -       IMPACT=LOW;STRAND=1
rs32076694      1:15833428      G       ENSMUSG00000025925      ENSMUST00000188371      Transcript      synonymous_variant      968     936     312     L       ttA/ttG -       IMPACT=LOW;STRAND=1

Here I picked four rows with two without SNP annotation (start with two dots) and two with SNP annotation (rs32076694, rs32076694). As you can see there are columns for 'protein position' (504, 504, 283, 312) and 'Amino_acids' (S, S, L, L). My question is whether there is an existing program that can help me retrieve a longer protein motif such like 10 amino acids centered on the mutated ones.

Answer 1

[Denise CS]

All I know is that there is an existing program that can give you the flanking sequence of the SNPs as As,Cs, Gs, Ts rather than amino acids. In BioMart, choose "Human Somatic Short Variants (SNPs and indels excluding flagged variants)", then under Attributes select Flanking sequences and enter the number of nucleotides. If you want 10 amino acids either way of the variant, choose 30 nucleotides both up and downstream. But you would then need to use another tool to translate from nucleotide to amino acid sequences.