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Ensemble Enzyme Prediction Pipeline (E2P2)
Version 3.1
December 15, 2016
=====================================================
We recommend downloading the tar.gz on Linux systems to avoid 
the unzip failure of zip format caused by "symlink error: File name too long".

Bug fixes:

1. Removed e-value (e-2) argument from blast run. The e-value argument in 
blast command had unexpected impacts. Better hits were sometimes not returned. 
The e-value cutoff is applied in a later step to filter all blast hits.  
2. To better support parallel run of E2P2 for multiple input sequence files, 
individual folder for hosting intermediate files is now created for each input.


Important reminder about input protein sequence fasta headers:
For E2P2 to run properly the fasta headers of input protein sequences 
should follow this format:
>unique_sequence_ID [followed by a “|” or a space before anything else]
 



Ensemble Enzyme Prediction Pipeline (E2P2)
Version 3.0
July 15, 2015
======================================================


What's new
----------
In version 3.0, E2P2 updated its BLAST and PRIAM programs to the latest 
versions. It uses RPSD 3.1 compiled recently as reference enzyme set. We 
adjusted the cutoff of BLAST and the ensemble scheme according to our 
assessment based on the new RPSD 3.1. 

E2P2 v3.0 also provides an additional output .orxn.pf file which 
translates EC numbers to their official reactions in MetaCyc reaction 
identifiers. Using this .pf file would prevent over propagation of EC 
numbers to all their descendent reactions by PathoLogic of Pathway Tools 
while creating pathway databases.

In the folder tools, we also provide some perl scripts for pre-process FASTA 
sequence files. 'cutter-fasta.pl' could be used to split huge sequence files 
into small ones to run E2P2 on them in parallel. 

'pf-EC-to-official-RXN.pl' is already built-in and needed as the final step
of runE2P2.py.

Description
-----------
The Ensemble Enzyme Prediction Pipeline (E2P2, version 3.0) annotates 
protein sequences with Enzyme Function classes comprised of full, four-part 
Enzyme Commission numbers and MetaCyc reaction identifiers. It is the enzyme 
annotation pipeline used to generate the species-specific metabolic databases 
at the Plant Metabolic Network (www.plantcyc.org) since 2013. E2P2 
systematically integrates results from two molecular function annotation 
algorithms using an ensemble classification scheme. For a given genome, all 
protein sequences are submitted as individual queries against the base-level 
annotation methods. E2P2 v3.0 used a custom database of annotated protein 
sequences, which we refer to as the Reference Protein Sequence Dataset (RPSD 
version 3.1). RPSD 3.1 contains approximately 50,182 enzyme and 91,855 
non-enzyme sequences, compiled from manually curated or experimentally 
supported data in UniProt/SwissProt (November, 2014 release), BRENDA 
(November, 2014 release), MetaCyc (November, 2014 release), and PlantCyc 
(November, 2014 release). The individual methods rely on homology transfer 
from RPSD 3.1 sequences, using single sequence (BLAST, E-value cutoff <= 
1e-2) and multiple sequence models (PRIAM) of enzymatic functions using 
custom profile libraries trained on enzyme sequence data annotated in RPSD 
3.1. The base-level predictions are then integrated into a final set of 
annotations using an maximum weighted integration algorithm, where the 
weight of each prediction from each individual method was determined via a 
5x3 nested cross-validation process. 

Installation
------------
The archived package is available from:
https://dpb.carnegiescience.edu/labs/rhee-lab/software

Unzip and extract the E2P2 package in your target location:
tar -xzf e2p2-3.0.tar.gz

Operation
---------
E2P2 was built to run on 64-bit Linux systems. As an in-house pipeline, it has 
not been tested widely on different systems. It relies on two individual 
methods, each of which has its own dependencies. All supporting programs, 
including dependencies, are bundled into the E2P2 package.

The input file containing protein sequence data must be in FASTA format.
Specify the paths of the input and output files and run E2P2 with the 
following command:
./runE2P2.py -i <input filename> -o <output filename>

For whole-genome datasets, we suggest partitioning the input sequence file
into subsets and running them in parallel in a distributed environment.

Contact us regarding questions and issues at curator@plantcyc.org.