Mitomaster Plugin
Mitochondrial data processing and analysis.%MMALLELE{. . .}%
Not implemented.%MMCONSERVATION{. . .}%
Not implemented.%MMFREQUENCY{. . .}%
Not implemented. Calculates allele frequency for the sequences currently in the database.%MMHAPLOGROUP{. . .}%
Not implemented. Retrieves haplogroup information for the sequences in the database. List? Table with counts and frequencies? Options for major and minor?%MMREFSEQ{. . .}%
Provides access to a mitochondrial reference sequence. Example: %MMREFSEQ{ start="1" end="10" }% evaluates to GATCACAGGT| Argument | Comment | Default Value | Example |
|---|---|---|---|
| start | Starting position. | 1 | start="127" |
| end | Ending position. Must be equal to or less than start. | 10 | end="132" |
| reference | The particular reference sequence. "rCRS" (the revised Cambridge sequence) is the only reference at present. This is a placeholder and does not have to be set. | rCRS | reference="rCRS" |
| species | "human" is the only species at present. This is a placeholder and does not have to be set. | human | species="human" |
%MMSEQ{. . .}%
Not implemented.%MMSTRUCTURE{. . .}%
Not implemented. Retrieves a structural diagram with the option to highlight certain positions.%MMTREE{. . .}%
Not implemented. Retrieves a tree image. Not sure about this one, but could be very useful for the haplogroup path I had considered.REST Interface
Not implemented. Test handler is working: http://mammag.web.uci.edu/bin/rest/MitomasterPlugin/mmseqPlugin Installation Instructions
- Install Bio::Mitomaster
- Make sure MitomasterPlugin.pm is in your plugin directory
- Run configure and enable the plugin
Plugin Info
| Copyright: | Copyright (C) 2009 MartyBrandon, marty.brandon@uci.edu |
| License: | GPL (GNU General Public License) |
| Version: | 4847 (2009-12-18) |
| Release: | 0.01 |
| Change History: | |
| 17 Dec 2009 | 0.01: Marty Brandon: Copied the EmptyPlugin to MitomasterPlugin and got basic functionality. Began defining the interface. Implemented MMREFSEQ |
You are here: System Web>Plugins>MitomasterPlugin
Topic revision: r4 - 18 Dec 2009 - 19:58:25 - MartyBrandon
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