How To Mask Low-Complexity Regions In Proteins?
1
4
Entering edit mode
14.0 years ago

SEG is built into BLAST to mask low-complexity regions in protein sequences before doing the sequence search. However, I don't want to use BLAST, I just want to mask my proteins. Does anyone know of a stand-alone version, or of a program that does something similar?

protein software • 6.1k views
ADD COMMENT
8
Entering edit mode
14.0 years ago
Paulo Nuin ★ 3.7k

AFAIK, dust and seg are included as stand alone tools in blast distributions, so you can use them independently from blast. I checked my local blast copy and it has dustmasker and segmasker.

Here's the output from a dry run with -help

segmasker -help

USAGE
  segmasker [-h] [-help] [-xmlhelp] [-in input_file_name]
    [-out output_file_name] [-infmt input_format] [-parse_seqids]
    [-outfmt output_format] [-window integer_value] [-locut float_value]
    [-hicut float_value] [-version-full]
DESCRIPTION
   Low complexity region masker based on the SEG algorithm
(...)
ADD COMMENT
0
Entering edit mode

Interesting. For some reason this was not included in the BLAST distribution that was installed on my system. Perhaps this is a difference between BLAST and BLAST+.

ADD REPLY
0
Entering edit mode

I think in the old days, wu-blast used to come with these too. And on NCBI version it was part of the NCBI toolkit.

ADD REPLY

Login before adding your answer.

Traffic: 2420 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6