Lincoln D. Stein

NAME

Bio::Graphics::Browser2::Plugin::RestrictionAnnotator - Generate a restriction map track in GBrowse

SYNOPSIS

In the appropriate gbrowse configuration file:

 plugins = RestrictionAnnotator

DESCRIPTION

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.

OPTIONS

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.

BUGS

None known yet.

SEE ALSO

Bio::Graphics::Browser2::Plugin

AUTHOR

Lincoln Stein <lstein@cshl.org>.

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.