I am trying to locate the orthologs of genes identified in a genome assembly in five other bird genomes (red-throated loon, adelie penguin, northern fulmar, chicken, pigeon).
To do this I made a blast database of each of the five genomes: makeblastdb -in '"Columba_livia.cds" "Fulmarus_glacialis.cds" "Gallus_gallus.cds" "Gavia_stellata.cds"' -out Expanded.txt -parse_seqids -dbtype nucl #new db
However, I am so far at a loss about how to search for each gene in my assembly and then return the best hit ortholog in all five genomes using local blast. I am new to running command-line blast and my best guess didn't work: blastn -query COLOgenes.fasta -db Expanded.txt -task blastn -dust no -outfmt "6 qseqid sseqid pident length qstart qend sstart send sallgi evalue qseq sseq" -evalue 1e-6 -num_alignments 1 -max_hsps 1 -out outputExpanded1.blast.txt
The most important thing is to get the actual sequence for each ortholog (should get five match sequences; one from each genome), but blast seems to only have options for returning one subject sequence.
Any ideas would be appreciated! Thanks, Zach