RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST
suite. The primary difference between this distribution and the NCBI
distribution is the addition of a new program "rmblastn" for use with
RepeatMasker and RepeatModeler.
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:
www.phrap.org )
- Support for cross_match-like masklevel filtering.
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