Bio::Graphics::Browser2::Plugin::RestrictionAnnotator - Generate a restriction map track in GBrowse
In the appropriate gbrowse configuration file:
plugins = RestrictionAnnotator
The RestrictionAnnotator plugin generates a series of automatic tracks showing restriction enzyme cut sites. For it to work properly, the genomic DNA must be loaded.
There are now config file options. The list of enzymes and their cut sites is contained in APACHE_CONFIG/gbrowse.conf/enzymes.txt, where APACHE_CONFIG is your Apache configuration directory. It is straightforward to add new enzymes. The format is:
<enzyme name> <recognition site> <cut site position>
For example, the entry for EcoRI is
EcoRI GAATTC 1
The "1" means that EcoRI will be cleaved at position 1, where positions are BETWEEN the bases starting with 0:
0 1 2 3 4 5 6 G A A T T C
The recognition site can be a regular expression.
None known yet.
Lincoln Stein <email@example.com>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.