aboutsummaryrefslogtreecommitdiff
path: root/academic/ncbi-rmblastn/README
blob: b203d952fa804ac2983af625c1529df6303986a8 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
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.