Blast "Max Matches In A Query Range" Option

Question

[ha.hassanzadeh]

Hi Everyone, This is the first time I'm going to try such a web site to see if it works or not, hope it works!

So I have a few questions regarding blast, I appreciate it if you can help me,

1. I see that blast has an evalue threshold option, is there a similar thing for percent identity? In other words is it possible to make it report only the hits with pident above a given threshold?

2. I see that in online version: there is an option "Max matches in a query range" how can I use the same thing in stand alone version? and what should I put in as the value for this key?

3. What is this option in standalone blast ? "-seg <string> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) "

I appreciate your help,

Answer 1

[dapregi]

Here are the answers for each question:

1. Option "-perc_identity" establishes a percent identity cutoff when doing blastn searches.

2. In order to limit the number of matches (HSPs) in a sequence, try "-max_target_seqs". It takes an integer (default value: 500).

3. SEG is a program for filtering low complexity regions in amino acid sequences. Residues that have been masked are represented as "X" in an alignment. This option is available in blastp, tblastn, tblastx and rpsblast searches.