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rhysf / Synima

Synteny Imager
MIT License
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non mRNA/gene features #3

Closed sejmodha closed 5 years ago

sejmodha commented 6 years ago

Hi There,

I was wondering if it is possible to include other features such as pseudogenes in the Synima analysis?

Thanks

rhysf commented 6 years ago

Hi @sejmodha ,

Providing you get those features into the required aligncoords and aligncoords.spans format - then it will work.

If using the Synima pipeline for ortholog prediction, then the feature you are interested in can be specified by the -f (feature) parameter of the first step of the ortholog prediction pipeline Create_full_repo_sequence_databases.pl

However, I think the feature will require a peptide and nucleotide sequence in the respective FASTA files to work.

One work around might be to create a pseudo peptide sequence (with the same IDs as the CDS FASTA) if one does not exist - and then make sure only CDS is used as parameters for the following ortholog prediction steps.

Hope that is useful. Rhys