Identify homolog sequences that appear in multiple RefSeq files
Hello,
I have a set of 4 RefSeq fasta files belonging to 4 different species. I'm trying to identify homologs that appear in all 4 RefSeq files. Whats the best and most efficient way to do that? Please note that I only want to identify sequences that are homologous in all 4 files.
1 answer
Depending on the species in your dataset, you can use any of the precomputed resources from NCBI
These resources provide FTP files that have either protein GI or accessions.
Or you could use one of the sequence clustering tools (BLASTClust, UCLUST or CD-HIT), though they can be less accurate.
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OrthoMCL might be helpful.
It might take a long time to run the whole analysis for all of your species.