I need help with a blast command, please help

Question

[neto.pvp]

I have this command:

blastn -db /home/BLAST_nt/nt -query otu_greedy_0.97_82.fasta -outfmt 5 -out otu_greedy_0.97_82_blastn.xml -evalue 0.001

And i have to include the following conditions:

percent identity of 95%, e-value of 0.001, minimum query coverage of 100%, best hit score edge of 0.05 and best hit overhang of 0.25.

should I include these conditions in the code above? if yes, how can i do that?

Answer 1

[Mensur Dlakic]

Your command already has all the conditions that can be specified, which is E-value threshold. The remaining options you want can't be set on command line.

I suggest you specify -outfmt 6 and save the output with an appropriate name. What can be included in the tabular output is specified here. Then you have to post-process this file by sorting according to the percent identity column (which is third from left if you use this format without modification) and removing all lines that have <95% in that column. For the other values you will have to be a bit creative and calculate them based on various quantities from the tabular output, but it should be doable.

This could be useful:

http://prodata.swmed.edu/hangout/

[neto.pvp]

Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!