using the Smith Waterman algorithm for blastn

[akshaya.ramesh]

Hello,

I have been working on some genome assembly and have just begun annotation of my the contigs. I am using blastn in blast+(ncbiv2.2.28) to help identify orthologous genes. I recently read a paper that soft filtering with SW algorithm were the most efficient in the identification of orthologous segments. I was wondering if there was anyway I could run blastn with the SW algorithm instead of X-drop algorithm? I am aware of the use_sw_tback parameter for blastp, but I would like to run my contigs through blastn and was wondering had any suggestions?

Any help/insights would be appreciated.

Thanks in advance.
Best,
Akshaya

[lh3]

Try ssearch from the fasta package. I do not know what's "soft filtering", though.

[rhinoceros]

If your ref genome is close enough, I'd say '-task megablast' will do the job just fine. As far as I know, there's no way to use SW with blastn..

[akshaya.ramesh]

Thank you for both your suggestions. This is very helpful.