pPAP: plant PKS Analysis and Prediction
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This directory contains a following file:
ppap.tar.gz: gzipped tar archive of pPAP

# Introduction

pPAP is a functional prediction tool for plant type III polyketide synthases (PKSs). [1]
The predicted functions are represented by "reaction types" defined by Shimizu et al. [2]
The reaction types consist of three features of reactions catalyzed by the PKSs:

(i) the starter substrate
(ii) extended structure of the polyketide intermediate
(iii) intramolecular cyclization

pPAP assigns each sequence of a query to one of four reaction types: R-4-A, R-4-C, R-2-X, or other.


# Reaction types used in pPAP

Reaction type:	R-4-A
Definition:	Ring-starter	4 methylenecarbonyl units in the intermediate	aldol cyclizaiton
Example of PKSs:	Stilebene synthase, Biphenyl synthase, and Bibenzyl synthase
Example of products:	Resveratrol, 3,5-Dihydroxybiphenyl, and 3,3',5-Trihydroxybibenzyl

Reaction type:	R-4-C
Definition:	Ring-starter	4 methylenecarbonyl units in the intermediate	Claisen cyclizaiton
Example of PKSs:	Chalcone synthase, Benzophenone synthase, and Homoeriodictyol/eriodictyol synthase
Example of products:	Naringenin chalcone, 2,4,6-Trihydroxybenzophenone, and Homoeriodictyol/eriodictyol

Reaction type:	R-2-X
Definition:	Ring-starter	2 methylenecarbonyl units in the intermediate	no cyclizaiton
Example of PKSs:	Benzalacetone synthase, Diketide-CoA synthase, and Curcumin synthase
Example of products:	p-Hydroxybenzalacetone, Feruloyldiketide-CoA, and Curcumin

Reaction type:	Other
Definition:	Other types than R-4-A, R-4-C, and R-2-X (e.g., Rn-4-Cn, Sb-4-C, Sc-7-A+, L-4-A, and etc.)
Example of PKSs:	Acridone synthase, Phlorisovalerophenone synthase, Aloesone synthase, Alkylresorcinol synthase, and etc.
Example of products:	1,3-Dihydroxy-N-methylacridone, Phlorisovalerophenone, Aloesone, Tetraketide alkylresorcinol, and etc.


# Requirement

pPAP is written in Ruby language.
This tool is intended for use on a Linux operating system and requires the following programs:

ruby >= 1.9.3	# Ruby language
bioruby >= 1.5.0	# Bioinformatics library for Ruby
mafft >= 7.270	# Multiple sequence alignment program
hmmer >= 3.1b2	# Analysis using profile hidden Markov models


# Set up

Install all the requisite programs and set PATH so that your shell can use them.

Extract the archive file "ppap.tar.gz"
% tar zxfv ppap.tar.gz

Then, the following directories and files will be created:

ppap/	
  ppap.rb	# Main program
  calculate_score_correlated_res_pair_ACX.rb	# Script for calculating correlation scores
  calculate_score_hmm_ACX.rb	# Script for calculating HMM scores
  LICENSE	# GNU GPL License Version 3
  README	# This file
ppap/data/	# Directory including 15 data files


# Usage

% ruby ppap.rb FASTA_FILE

FASTA_FILE: a query amino acid sequence file in (multi) FASTA format.

# Changelog

Ver. 1.1 (2018/12/13)
  Update for new version of MAFFT

Ver. 1.0 (2017/1/25)
  First released version

# License

Copyright (c) 2016 Yugo Shimizu
Bioinformatics Center, Institute for Chemical Research, Kyoto University
pPAP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
as published by the Free Software Foundation, either version 3 of the License, or any later version.
A copy of the GNU General Public License Version 3 is included in the archive as "LICENSE".

# References

[1] Shimizu,Y. et al. (2017) Discriminating the reaction types of plant type III polyketide synthases. Bioinformatics, 33, 1937-1943.

[2] Shimizu,Y. et al. (2017) Type III polyketide synthases: functional classification and phylogenomics. ChemBioChem, 18, 50-65.

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Last update: 2018/12/13