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Filter Out Only Ccds (Consenses Cds) Sequences From List Of Ensembl Transcripts

I have a list of mouse Ensembl gene IDs in the form of: 

ENSMUSG00000022973

I input them into http://biodbnet.abcc.ncifcrf.gov/ to extract all of the transcript IDs that correlate with the gene IDs to get:

ENSMUST00000118246
ENSMUST00000170853
ENSMUST00000129743
ENSMUST00000129041
ENSMUST00000121759
ENSMUST00000130813
ENSMUST00000154276
ENSMUST00000125032
ENSMUST00000156140
ENSMUST00000118390

Only two of these have a CCDS, namely:

ENSMUST00000121759
ENSMUST00000170853

How can I filter these out for ALL of the transcripts associated with ALL of the gene IDs?

cds sequence ensembl
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updated by Biostar Biostar • written by hicsuntdrac0nis • hicsuntdrac0nis

This post is being closed because OP has not been seen in 6+ years

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written by Ram Ram

1 answer

I don't believe there is a pre-packaged tool or website that can do this. If doing it manually is out of the question, then you can try writing a script to query the NCBI website to see if transcripts on your list have a CCDS, or you can download the data and then compare your list vs the downloaded data directly with something like R.

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written by pstew pstew

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