Lincoln D. Stein > GBrowse-2.55 > Bio::Graphics::Browser2::Plugin::RestrictionAnnotator

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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.

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