How To Check Whether Snps Are In Helices Or Beta-Strands Or In Coils?

Question

[bioinfo]

From the generated SNP vcf file by BWA and GATK, I have located the SNPs in exons, introns and pseudogenes. Now I want to locate where exactly in the secondary structure these SNPs are. Is there any tools I can use to do it?

Answer 1

[Pierre Lindenbaum]

My VariationToolkit contains a tool that fetches the features from uniprot.org. It just needs the ACN of the protein and the position of the amino acid:

$ echo -e "#POS\tID\n54\tQ04721\n1\tHELLO\n166\tP03536" |\
    uniprot -p 1 -s 2 |\
    verticalize 
#warning: Cannot find record for HELLO
>>>     2
$1      #POS                    54
$2      ID                      Q04721
$3      uniprot.beg             26
$4      uniprot.end             2471
$5      uniprot.type            chain
$6      uniprot.status          .
$7      uniprot.desc            Neurogenic locus notch homolog protein 2
$8      uniprot.evidence        .
$9      uniprot.ref             .
<<<     2

>>>     3
$1      #POS                    54
$2      ID                      Q04721
$3      uniprot.beg             26
$4      uniprot.end             1677
$5      uniprot.type            topological domain
$6      uniprot.status          potential
$7      uniprot.desc            Extracellular
$8      uniprot.evidence        .
$9      uniprot.ref             .
<<<     3