Snps In Protein Domains

Question

[Dataminer]

Hi!

I have a list of genomic coordinates along with the mutations that have occurred. Something like this:

chromosome    13    27470642    C    G
chromosome    13    27890643    C    A
chromosome    13    27490642    -    C
chromosome    13    27360641    C    AG

I would like to know, on which protein domains these are present ?

Does anyone know , how this can be queried?

Thank you

Answer 1

[Emily]

Have you looked at the Variant Effect Predictor?

[Pierre Lindenbaum]

cool, I didn't know the "- -domains" option. :-)

Answer 2

[Pierre Lindenbaum]

I wrote a tool called MapUniprotFeatures

It loads the UCSC knownGenes database, parses a XML definition of uniprot and produce a BED file of all domains.

You can then get the intersection of your ~VCF with this BED file with bedtools:

$ java  -jar dist/mapuniprot.jar \
    REF=/path/to/human_g1k_v37.fasta \
    UNIPROT=/path/uri/uniprot.org/uniprot_sprot.xml.gz  \
    kgUri=<(curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk -F '        ' '{if($2 ~ ".*_.*") next; OFS="       "; gsub(/chr/,"",$2);print;}'   ) |\
    LC_ALL=C sort -t '  ' -k1,1 -k2,2n -k3,3n  | uniq | head


1   69090   69144   topological_domain  1000    +   69090   69144   255,0,0 1   54  0
1   69144   69216   transmembrane_region    1000    +   69144   69216   255,0,0 1   72  0
1   69216   69240   topological_domain  1000    +   69216   69240   255,0,0 1   24  0
1   69240   69306   transmembrane_region    1000    +   69240   69306   255,0,0 1   66  0
1   69306   69369   topological_domain  1000    +   69306   69369   255,0,0 1   63  0
1   69357   69636   disulfide_bond  1000    +   69357   69636   255,0,0 1   279 0
1   69369   69429   transmembrane_region    1000    +   69369   69429   255,0,0 1   60  0
1   69429   69486   topological_domain  1000    +   69429   69486   255,0,0 1   57  0
1   69486   69543   transmembrane_region    1000    +   69486   69543   255,0,0 1   57  0
1   69543   69654   topological_domain  1000    +   69543   69654   255,0,0 1   111 0

[Dataminer]

from where I can get this uniprot_sprot.xml.gz? Thank you

[Pierre Lindenbaum]

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz

[Dataminer]

Hi!

I am trying to download the file from github and it is throwing up tis error:

git clone git://github.com/lindenb/jvarkit/wiki/MapUniProtFeatures

Cloning into 'MapUniProtFeatures'...
fatal: remote error:
  lindenb/jvarkit/wiki/MapUniProtFeatures is not a valid repository name

[Pierre Lindenbaum]

git clone https://github.com/lindenb/jvarkit.git

Answer 3

[Pablo]

You can just use SnpEff's NextProt option

http://snpeff.sourceforge.net/SnpEff_manual.html#NextProt