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Ferret Plugin

Contents

  1. Description
  2. Usage
  3. Config Tree
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Description

(The Ferret plugin is not provided in newer version of GOBU, please refer our source repository if you are interested.) This is a customized plugin for our on-going EST annotation project. This plugin includes a sequence window and a zebrafish genome drawing window.
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Usage

  1. Fig. 1
    Plugins -> Ferret plugin. A window called "FerretPlugin Main Window" will appear, usually in the upper-left corner of your screen.
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    Fig. 2
    Click Sequence Window button, then a window called "Ferret - Sequence" will appear. This window will display sequence information of user selection.
  3. Click Zebrafish Genome View button, then a window called "Ferret - Zebrafish Genome View" will appear. This window will show all zebrafish genome.

    Generally speaking, the usage of this window is almost the same with Genome View window of Genome View Plugin except the additional Confidence filter option.

    Once the Confidence filter is checked (i.e. selected), every new incoming drawing will be restricted to best LOC P-node (i.e. most confident and longest LOC P-node).
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    Fig. 3 Fig. 4

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Config Tree

<ItalicString> means a variable.

This plugin obtains zebrafish chromosome lengths from config tree. A descendant GenomeName P-node called "Zebrafish" under Genome Information P-node must be provided. Under GenomeName P-node "Zebrafish", normal child nodes must in the form <chromosome name>:<chromosome length>.

See file "ZebrafishChrInfo.tree" in config sub-folder for examples.