How to use a different window size for TBLASTN?

Question

[islama]

Hi, I am relatively new user of BLAST. I am trying to use a different window size than the default 40 for comparison with another local alignment tool. But no luck so far. Is there any way to define a different window size for TBLASTN? Any help would be highly appreciated.

Answer 1

[Philipp Bayer]

I assume you're using command-line blast+

tblastn -help says:

-window_size <integer, &gt;="0"> Multiple hits window size, use 0 to specify 1-hit algorithm

[islama]

Thanks for the reply. However, I am not using BLAST+ bcoz my interest is Tblastn.
I have tried following commads and got the following error:
blastall -i <query_file.fa> -d <db_file.fna> -W 3 -p tblastn -o <output_file> -window_size 20
[blastall] ERROR: Frame shift penalty (OOF algorithm for blastx) [indow_size] is bad or out of range [? to ?]
Any idea what went wrong? Meanwhile, I am following this link: http://www.ncbi.nlm.nih.gov/books/NBK279675/.

[Philipp Bayer]

I see you're using the "old" blast then

The -window_size flag is only for the "new" blast+, in the "old" one it's -A:

-A Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer] default = 0

[islama]

Thank you. It worked.