Hi, i am looking for organisms in a clade (here: firmicutes), that have one gene (say A) but lack the other (B). Whille I can easily find organisms that have gene A via BLAST search, I am struggling with the second constrain. Manually checking each organism found in A in a subsequent BLAST search with B as a query obvioucvsly is not an option. I tried blasting gene B too and compairing the lists of resulting organisms, but since the lists are not complete and only show the first 50/100 hits, this approach was unsuccessful.
Any suggestions on this problem? Thanks in advance.
Also note that both genes A and B may have multiple paralogs and are poorly/incensistently annotated, so comparison needs to be on the sequence.
