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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
Faculty/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.