Matching and Converting Transcript/Protein id to Gene ID (Ensemb. Plants) - MCScanx input
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4.5 years ago
venura ▴ 70

Hi,

I am trying to generate blast input file to MCScanX. What I did so far is ;

  • Downloaded latest solanum genome files (fasta amd gff3) from ensembl plants. Genome of interest is Potato.
  • I have created local blast (protein) database

However, now I am stuck because; -protein sequences are given based on the transcript id (as an example PGSC0003DMT400087821) but gene id (PGSC0003DMG400037392) is completely different from transcript id. So I wont be able to match the output with gene ID as required by the program.

end of the day what I need is protein sequences based on the gene ID rather than transcript id.

Is there a way to overcome come this naming mismatch? Thank you,

ensembl • 1.3k views
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But genes have multiple transcripts and therefore multiple proteins. If you link your protein sequence to gene IDs, you will get multiple sequences with one ID. How would that work?

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I agree. But MCScanX accept only gene names. Workflow include blastp against the genome followed by the synteny analysis. What I want to do is identify segmental and tandem duplications in potato genome and MCScanX is the most recommended tool i found so far.

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Hi, have you find the solution for it ?

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