(I am a complete newbie to bioinformatics, so please bear with me!).
I recently used BLAST to compare a 500 bp nucleotide sequence in S. cerevisiae to a bunch of other 500 bp nucleotide sequences in various fungi (these other sequences are homologs of the S. cerevisiae gene). Ideally, when I click "BLAST", I want to get nothing back. What I'm trying to double check is the assumption that my S. cerevisiae sequence is NOT similar to my other input sequences.
Here's what I ran on the computer, using the BLAST website:
After I run this query, I only get one sequence back:
which tells me that the sequence I got as an output needs to be excluded from my dataset, as it's too similar to the S. cerevisiae sequence.
The problem is, I need to run this type of query and analysis about 6000 more times for 6000 different S. cerevisiae genes and their homologs. I don't know how to do this programmatically. The Biopython packages seem to only compare one sequence against the whole NCBI database, and I was really struggling to understand how to do this via the command line (was struggling with the package installations a bit, and it also seemed to only be for one sequence input).
Is what I'm doing here a multiple sequence alignment? When I looked into programmatically doing an MSA, the output seemed to only be the alignment, but I want to see an output like the website gives me. I'm not really sure what I should be looking into.
Any guidance would help!