BLAST+ vs Web BLAST "Automatically adjust parameters for short input sequences" command line arg

Question

[oostin623]

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.

Answer 1

[Andrzej Zielezinski]

The option "Automatically adjust parameters for short input sequences" on the NCBI site is compatible only with the blastn program. So for example, if you select megablast on the website and your query sequence is short, BLAST will automatically switch to blastn (blastn-short). If you want to make sure this is the case, go to the BLAST website, provide some short sequence and choose megablast. Once your results are displayed, click on the Search Summary at the top of the page and you will see something like this:

Search Parameters

Program                blastn
Word size              7
Expect value           1000
Hitlist size           100
Match/Mismatch scores  1,-3
Gapcosts               5,2
Filter string          F
Genetic Code           1

[duliuwen]

The search summary will shows "Program blastn" no matter what the -task (megablast,blastn,dc-megablast) is when you use nucleotide blast, because they are different task types of blastn(nucleotide blast) .