Orthology - Link Ensembl ID with CCDS ID

Question

[newbie42]

Hi, I'm a newbie. I'm working on mouse/human orthology and I need to link some CCDS ID with Ensembl ID.

I have two .csv files A and B.

File A contains lines with Ensembl ID of type ENSP (Protein stable ID):

Splice variant  Gene              ...
ENSP00000135185 ENSG00000047284   ...

File B contains lines with CCDS ID:

HumanEns        MouseEns           HumanCCDS MouseCCDS ...
ENSG00000000005 ENSMUSG00000031250 CCDS14469 CCDS30386 ...

I want to identify which splice variant are in both of files: For example: is the transcript ENSP00000135185 also in file B?

Thank you for your help and please let me know if this question was already answered. I searched the web and didn't find anything.

Regards,

Answer 1

[newbie42]

Hi again,

Before posting here I had tried to find the correspondence between CCDS and ENSP via Ensembl Biomart (online tool). Unfortunately I did not find any protein or variant with a CCDS identifier. This morning I thought about it again and ran the exact same query in an older Ensembl database (2016) and there I got the desired match list. It looks like this:

CCDS ID   Ensembl Protein ID
CCDS9679  ENSP00000344579
CCDS43854 ENSP00000346670
CCDS55329 ENSP00000361397
CCDS47961 ENSP00000393683 ...

I will now write a small script to use this correspondence and solve my initial problem.

Hopefully it will be useful to someone someday,

Regards,