Project

bio-plasmoap

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The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.
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 Popularity
Downloads
15,521
Stars
1
Forks
0
Watchers
3
 Releases
Current version
0.1.1
Total releases
4
First release
2012-01-06
Latest release
2016-04-14
 Development
Primary Language
Ruby
Licenses
MIT
Average date of last 50 commits
2014-02-04
Reverse Dependencies
0

 Dependencies

Development

bundler
>= 1.0.0
jeweler
>= 1.6.4
shoulda
>= 0
test-unit
>= 3.1.8

Runtime

bio
>= 1.4.1
bio-signalp
>= 0.2.0
 Project Readme

bio-plasmoap¶ ↑

PlasmoAP is a program for predicting apicoplast targetting sequences in Plasmodium falciparum (the most fatal causative agent of malaria). This biogem implements the PlasmoAP algorithm, designed from the PlasmoAP journal article:

Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum.
Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS, Cowman AF, McFadden GI.
Science. 2003 Jan 31;299(5607):705-8.
PMID: 12560551

PlasmoAP requires the bio-signalp BioRuby plugin to be installed and therefore SignalP itself. See github.com/wwood/bioruby-signalp for more details.

Specifically, it requires version 3 of SignalP.

Installation and usage¶ ↑

To install:

gem install bio-plasmoap

To use:

plasmoap.rb /path/to/proteins.fasta

Copyright¶ ↑

Copyright © 2012-2016 Ben J Woodcroft. See LICENSE.txt for further details.