Question: Easy Way To Map Cds Coordinates To Genomic Coordinates
gravatar for Alper Yilmaz
9.6 years ago by
Alper Yilmaz90
Alper Yilmaz90 wrote:

Suppose that I have a protein domain in my GeneA, and I know coordinates of the domain within the cds sequence of GeneA. In addition, I know the genomic coordinates of GeneA (eg, in GFF format) along with mRNA, exon coordinates.

Is there a easy way, to map the protein domain coordinates to genomic exon coordinates?

I looked into Bio::Coordinate::GeneMapper but was not able figure out it.

cds gff coordinates mapping bed • 4.8k views
ADD COMMENTlink modified 8 months ago by Shicheng Guo8.4k • written 9.6 years ago by Alper Yilmaz90
gravatar for brentp
9.6 years ago by
Salt Lake City, UT
brentp23k wrote:

If you're not tied to perl, this is something that pygr does quite nicely.

E.g. this example or this one

Basically, you add an annotation to a sequence and then it keeps track of local and global positions and strand orientation.

There's an example here where they load data from a gff file. And there's a class specifically for protein annotations.

I believe the workflow would be something like:

  1. add the proteins and the exons each in their own annotationDB
  2. query for the protein to get a particular global location
  3. use that global location to query to get the exonic coordinate.
ADD COMMENTlink written 9.6 years ago by brentp23k

could you show an example of how pygr does the transformation from genomic to codon space given an annotation of coding exons? I looked at the docs you linked to but it seems very sparse/opaque. there's no explanation of the translation class or an example of the global to local transformation so i'd be very interested to see a simple example.

ADD REPLYlink written 8.1 years ago by user850
gravatar for Shicheng Guo
8 months ago by
Shicheng Guo8.4k
Shicheng Guo8.4k wrote:

You can receive the full genomic position for all the conserved domains with jvarkit and then use bedtools to find domains for your specific gene.

git clone

cd jvarkit

./gradlew mapuniprot



java -jar ~/hpc/tools/jvarkit/dist/mapuniprot.jar  -R ~/hpc/db/hg19/hg19.fa  -u ~/hpc/uniprot_sprot.xml.gz -k knownGene.txt.gz -o uniprot_sprot.bed
ADD COMMENTlink modified 8 months ago • written 8 months ago by Shicheng Guo8.4k
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