blastn doesn't consider the entire sequence

Question

[chrisothal]

When I BLAST two sequences with a mismatch at position 3 using NCBI's servers and selecting "somewhat similar sequences (blastn)" as an option, I get a report that begins at base 1. However, when I use the command line BLAST+ to perform the same alignment, I get a report that begins at base 4 after the mismatch. How can I modify the command line version to mimic what NCBI's servers are doing?

blastn -query ref.fa -subject clone.fa

I noticed that NCBI is using BLASTN 2.2.31+ while my current version is 2.2.30+. Does that make all the difference?

Answer 1

[utzermel]

If you want to perform a command-line BLAST with exactly the same parameters as on the NCBI servers, you can download the BLAST parameters as a search strategy file and supply it as an argument to the command-line program. Likely, if you don't supply the same parameters that are used online for "somewhat similar sequences" you will not get the same result, as they are probably different from what is set as defaults in the command line.

Just download the search strategy after conducting the search and add it to your command.

blastn -import_search_strategy search_strategy.asn -query ref.fa -subject clone.fa

This should then yield the same result locally.

Answer 2

[h.mon]

Use

-task="blastn"

The default for the command-line is

-task="megablast"

Did you change any parameter?