Question: Easy Way To Map Cds Coordinates To Genomic Coordinates
2
gravatar for Alper Yilmaz
7.6 years ago by
Alper Yilmaz90
Turkey
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 • 4.0k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 7.6 years ago by Alper Yilmaz90
3
gravatar for brentp
7.6 years ago by
brentp22k
Salt Lake City, UT
brentp22k 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 7.6 years ago by brentp22k

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 6.2 years ago by user780
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1829 users visited in the last hour