I have the amino acid sequence of a gene of interest. I want to identify all the different homologs in different species, and assemble it in a single FASTA file format. Which I then want to input into a sequence similarity network (SSN) tool, to find how the different homologs from different species cluster.
My problem is: how do I get this list of homologs into one FASTA file? I tried two approaches. One is find the protein on Kegg database, then I click on 'Orthologs'. This gives all the homologs in the KEGG database (about 2500). But I don't see a way to download the amino acid sequences in one go, unless I click each homolog indvidually and copy the aa sequence.
The second option is to do a BLASTP usign RefSeq as the search database. This gives me only a limited number of hits (restricted to 100), and furthermore, I still can't figure out how to download the FASTA sequences of the hits in one go.
Can someone please offer some help? Thanks in advance!