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

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NAME ^

Bio::Graphics::Browser2::Plugin::Blat -- plugin to map sequences against the genome

SYNOPSIS ^

 in human.conf:

[Blat:plugin] blat_executable = /usr/local/gfClient 2bit_dir = /project/gbrowse/2bit_genomes host = blat.server.host.name port = 17780

 in mouse.conf:

[Blat:plugin] blat_executable = /usr/local/gfClient 2bit_dir = /project/gbrowse/2bit_genomes host = blat.server.host.name port = 17781

DESCRIPTION ^

This Gbrowse plugin will take a sequence (entered in the configuration screen) and BLAT it against the genome of the current organism ( port from conf file).

You must, of course, have the Blat server(gfServer) and client(gfClient) installed, and you must set plugin parameters in the conf file: [Blat:plugin] blat_executable = /path/to/your/blat_client

The plugin only works with default psl output format for the moment.

AUTHOR ^

Sean O'Keeffe <okeeffe@molgen.mpg.de>.

AUTHOR ^

Sean O'Keeffe <okeeffe@molgen.mpg.de>.

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