How To Mask Low-Complexity Regions In Proteins?

Question

[Michael Kuhn]

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?

Answer 1

[Paulo Nuin]

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
(...)

[Michael Kuhn]

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+.

[Paulo Nuin]

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.