How To Get Flybase Gene Id According To Kegg Gene Id?

Question

[Dejian]

I got a list of kegg gene ID for fruitfly. Now I want to get these sequences. I think mapping these KEGG gene ID to flybase gene ID and then extracting the sequences from flybase is a good way to do the job. I am sure there is a map between kegg gene id and flybase gene id (see below), however, I do not know where it is. Give me a hint? Thanks!

Dmel_CG10219 <> FBgn0039112

Dmel_CG10320 <> FBgn0034645

Answer 1

[Casey Bergman]

The CG identifiers are not Kegg gene ids but the FlyBase Computed Gene IDs. The CG id nomeclature was inherited from Celera/Berkeley and then gene model names were rationalized into the FlyBase paradigm, where all object types are given a FBxx id, where FB=FlyBase and xx=object type (in this case, gene name).

To get a mapping between CGids <-> FBgns, use biomart, with this query.

[Dejian]

Thanks, Casey. The query you provided is right what I want.

Answer 2

[Lars Juhl Jensen]

If you have KEGG gene IDs, and you want to get the sequences, why not simply download the sequences from KEGG and save yourself the painful and error-prone mapping exercise?

You can download them all from the KEGG FTP site: ftp://ftp.genome.jp/pub/kegg/genes/organisms/dme/

[Dejian]

You are right. This is the most convenient way to do my current job. Many thanks, Lars.

Answer 3

[Joachim]

You are accessing the FlyBase database directly, right?

CG10219 and CG10320 are synonyms in FlyBase, which you can use to get the FlyBase gene ID as follows:

SELECT DISTINCT
    f.uniquename
FROM
    feature f,
    synonym s,
    feature_synonym fs
WHERE
    s.name = 'CG10219'
    AND
    s.synonym_id = fs.synonym_id
    AND
    f.feature_id = fs.feature_id
    AND
    f.organism_id = 1;;

Some explanation:

• You need DISTINCT because there are several mappings in feature_synonym that match the same synonym_id and feature_id, but differ in pub_id (otherwise it will just return the FlyBase ID a couple of times)
• You need to match organism_id because otherwise you get non-dmel results too

[Dejian]

No. I am trying to download a batch of sequences from the website of FlyBase. The batch download accepts IDs like CG.However, a CG-like ID ofen corresponds to more than one FBgn ID and only one of them is what I want. Thus, it is inconvenient to use the batch download on the website. Any other method? Thanks.