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?
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written
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Michael Kuhn
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
(...)
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+.
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.
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