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