How to extract the CDS from a fasta file using the protein IDS ?
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5 days ago
sunnykevin97 ▴ 760

Hi,

Finally, end up with good amount of orthologs (1500).

I'd like to extract the CDS of the protein sequences ?

Given a IDS.protein.txt file, I'd like search against the CDS sequences of all the 10 species.

For example -

cat  IDS.protein.txt

>g66422.t1
>XP_034399799.1
>g40125.t1
>g66683.t1
>g53726.t1
>g25019.t1
>g26815.t1
>LipSG014613.t1
>hadal41775
>evm.model.Contig3137_pilon.3_pasa2.longest.filter_rm

I'm interested in searching the 1st ID against the 1.fasta file, and 2nd ID against 2.fasta file

extracting ---

>g66422.t1 (1st ID) vs. **1.fasta**
>XP_034399799.1 (2nd ID) vs. **2.fasta**
....
....
....
....
>evm.model.Contig3137_pilon.3_pasa2.longest.filter_rm (10th ID) vs. **10.fasta**

Some suggestions please.

gene genome protein • 93 views
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