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NCBI RMBLASTN

NCBI RMBLASTN

RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
Support site:
http://www.repeatmasker.org/RMBlast.html
Eligibility
Consultants/PTSAs
Faculty
Post-Docs
Researchers
Staff
Students
License Type
Freeware
Installation instructions

Linux installation instructions

Use modules to load the applications available in the scientific application stack.
Please contact IT Linux Support or open a ticket with the IT Help Desk to install a new version of this application.

Loading NCBI RMBLASTN from the scientific application stack

$ module load ncbi-rmblastn
$ <execute one of the blast commands>
Features

RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:

  • Support for custom matrices ( without KA-Statistics ).
  • Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
  • Support for cross_match-like masklevel filtering.