Easy Way To Map Cds Coordinates To Genomic Coordinates

Question

[Alper Yilmaz]

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.

Answer 1

[brentp]

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.

[user]

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.

Answer 2

[Shicheng Guo]

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

cd jvarkit

./gradlew mapuniprot

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

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

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