commandline blast

[kaps]

Dear all,

I am conducting a BLASTN (commandline) on my viral contigs. My study is about virus discovery. I have so far used the default settings for HIGHLY SIMILAR BLASTN search. I am wondering whether this will give appropriate results.

Please advise!!

[GenoMax]

What do you think? Have you looked at the results you have so far? You have listed the limitation of the type of search you did above. Is your aim to locate known viruses or sequences that *may* represent, so far unknown viral species?

[kaps]

I am getting some interesting results but wanted another opinion from the forum!
My aim is to identify viruses that could be in the samples (known or unknown).