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      Sequence Profiles for Secondary Structure & Solvent Accessibility Prediction (PROFILpro)

                             Method Description & Project Documentation

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Author(s) :  Christophe Magnan (cmagnan@ics.uci.edu)
Copyright :  Institute for Genomics and Bioinformatics
             University of California, Irvine
Modified  :  2015/07/02

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                                         Method Description
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PROFILpro is a small utility to generate the input sequence profiles for secondary structure and
solvent accessibility prediction tools SSpro, SSpro8, ACCpro, and ACCpro20. PROFILpro is basically
a simple extension of the BlastPGP software accepting large input fasta files and processing the
sequences on several cores instead of a single thread. Outputs of the blastpgp program are also
post-processed to generate a normalized profile sum of 1 for any amino acid in input. The number
of iterations (or rounds) to perform on the reference protein database is an input of the program
and is limited to 2, 3, or 4. The database used to generate the sequence profiles is UNIREF50 but
other databases can be added by simply editing the project profile and a few bash scripts.

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                                        Project Documentation
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This section provides a description of the project folder and how to use PROFILpro.

=========================================  Project Folder  =========================================

A brief description of the project folders is given below.

- bin             Main script to run PROFILpro
- data            Reference protein datasets for PROFILpro
- doc             Documentation of the software
- env             Bash profile for running PROFILpro
- lib             PROFILpro scripts to generate sequence profiles
- tmp             Temporary work folder for the software
- tools           Third-party tools used by PROFILpro

=========================================  Software Usage  =========================================

PROFILpro comes with only one script located in the 'bin' folder: generate_profiles.sh

Usage:  ./generate_profiles.sh  input_fasta  output_profiles  num_rounds  [num_threads]

With:

- input_fasta        Input protein sequences in FASTA file format
- output_profiles    Output file for the sequence profiles
- num_rounds         Number of blastpgp iterations on UNIREF50 (2, 3, or 4 only)
- num_threads        Number of cores to use to process the input dataset (default=1)

=======================================  Input Files Format  =======================================

Input files must be in the standard FASTA file format. There is no limit for the number of input
sequences to process beside the amount of RAM memory available on the machine running the program.

====================================  Output Files Description  ====================================

Sequence profiles are written in the following file format for each input protein sequence:

>sequence header                 // As provided in the input fasta file
amino_acid_1 profile_values      // Profile for the first amino acid of the protein sequence
amino_acid_2 profile_values      // Profile for the second amino acid of the protein sequence
...                              // ...
amino_acid_n profile_values      // Profile for the last amino acid of the protein sequence

The 20 profile values reported after the input amino-acid character are space-separated and
given in the same order than blastpgp output files: A R N D C Q E G H I L K M F P S T W Y V

The profiles are reported in the same order than the sequences in the input fasta file,
one after each other following the format described above for each sequence.

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                                           Release Notes
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Version 1.1 (2015)

Author      :  Christophe Magnan
Description :  Bug fixes for version 1.0
Comments    :  Non-standard amino acids replaced by X
               Sequences of length greater than 10,000 ignored

Version 1.0 (2013)

Author      :  Christophe Magnan
Description :  First release of the software
Comments    :  Shared tool for SCRATCH-1D, SSpro, SSpro8, ACCpro, ACCpro20, and HOMOLpro.

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