I am trying to search some short sequences using Geneious
blastp search with the standard parameters.
The problem is that Geneious does not automatically detect for small sequences (the BLAST website does!). Therefore, I am looking for the equivalent of the blastp parameter
short queries (automatically adjust parameters for short input sequences). Does this exist as a command line argument? Alternatively, but even more conveniently, does Geneious have this parameter hidden away somewhere in its interface?
Thank you very much for your answers.
Edit: I found this Link on the Geneious website (unfortunately focused on
blastn). It mentions the weakness of Blast when it comes to short sequences; however, as the option in
short queries exists, I still hope that there is a viable solution.