Mapping Orthologs On Fasta Files

Question

[Gorysko]

Dear all

Last week I was looking for method of searching orthologs and have found quite good python script for this - RSD. But now I have other question. I have a list of orthologs and fasta file - is it possible to map orthologs on this fasta file for next visualization in genome viewers.

[Neilfws]

You need to provide more details. What is the list of orthologs? Just a list of identifiers of some kind? What's in the fasta file - DNA sequence, protein sequence? What do you mean by "map onto file"? For genome viewers, you probably need coordinates of some kind - do you have those?

[Gorysko]

I have a list of identificators and list of sequences. In "mapping" I understand to add some feature on genbank file

Answer 1

[Ahdf-Lell-Kocks]

If what you mean is that you want to visualise your orthology relationships to the genomic fasta file, you can generate a GFF file from your list of orthologs and then visualize it with a program like IGV or similar.