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
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
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