I am building a web interface to reproduce the NCBI web BLAST form options to use for local BLAST+ searches. I am trying to map each field on the NCBI website's searches to the command line argument for that parameter in BLAST+.
Where I'm having trouble is blastn, specifically the "Automatically adjust parameters for short input sequences" check box on the NCBI site. There are 3 algorithm radio buttons and this check box, so the auto adjust for short sequences is compatible with all 3 search algorithms, blastn, megablast, and disc-megablast.
Now with BLAST+, there are instead 4 algorithm options, selected using the -task flag. The 4th extra one is "blastn-short". There also seems to be no flag to specify "adjust for short sequences".
Is selecting the task "blastn-short" the equivalent to using the blastn algorithm with the checkbox checked on NCBI? If so, how do you adjust for short input sequences with the other 3 search algorithms then?
Thank you for any insights on this matter.