This is the README file for PARTS version 12.19.09.12.42.07

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This document includes following about PARTS program:
1) Legal Notice
2) Description and Citation
3) Installation
4) Usage 

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1) Legal Notice

   Copyright 2007-2008-2009 Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews.

   This file is part of PARTS.


   PARTS 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
   (at your option) any later version.

   PARTS is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with PARTS.  If not, see <http://www.gnu.org/licenses/>

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2) Description and Citation

PARTS is a pairwise RNA secondary structure and alignment prediction program.

PARTS 12.19.09.12.42.07 - See CHANGES for differences in previous versions.
PARTS is distributed under GNU general public license, please refer to COPYING
for license terms and conditions!

Citation:
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
PARTS: Probabilistic Alignment for joinT Structure prediction,
Nucleic Acids Res., April 2008; 36: 2406 - 2417. 

Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
Stochastic sampling of the RNA structural alignment space
Nucleic Acids Res., July 2009; 37: 4063 - 4075. 

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3) Installation

Run make under PARTS/ directory. PARTS is built under release. 

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4) Usage

PARTS can be run in 3 modes:
1. MAP mode: Computation of structural alignment with maximum a posteriori probability
2. PP mode: Computation of posterior probabilities of base pairing
3. Stochastic Sampling mode: Stochastic sampling structural alignments from pseudo-Boltzmann ensemble

For all the other options, type PARTS on command line.

Example:
a) Build PARTS as described above.
b) cd to release/ directory.
c) type:

./PARTS input/RD0260.seq input/RD0500.seq -map

OR

./PARTS input/RD0260.seq input/RE2140.seq -pp

OR 

./PARTS conf.txt

d) PARTS should start running, with the progress bar moving on command line.
e1) MAP output structures are output to release/ directory, respectively.
e2) Posterior probabilities are output to release/ directory

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Configuration file format:
Configuration file (named conf.txt in the above example), is formatted as a multi line ascii file
such that each line contains "[option] [value]", specifying a value for the option. "seq1", "seq2", and
"mode" are mandatory options. The values are the same as command line values for corresponding options. 

For example:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
seq1 RD0260.seq
seq2 RE2140.seq
seq1_op_prefix RD0260
seq2_op_prefix RE2140
mode stochsample
n_samp 1500
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

makes PARTS do a stochastic sampling of 1500 structural alignments (1500 structures for each sequence and 
1500 alignments) for sequence data in RD0260.seq and RE2140.seq. 

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Output file naming:
PARTS uses prefixes for each sequence to generate output file names. By default, the 
prefixes are set to "seq1" and "seq2". The prefixes can be specified at the command line 
by -seq1_op_prefix and -seq2_op_prefix respectively. For instance:

./PARTS input/RD0260.seq input/RE2140.seq -map -seq1_op_prefix RD0260 -seq2_op_prefix RE2140

Computes the MAP structural alignment for RD0260.seq and RE2140.seq and generates output files:
RD0260_map_ct.ct
RE2140_map_ct.ct
RD0260_RE2140_map_aln.aln

And;

./PARTS input/RD0260.seq input/RE2140.seq -pp -seq1_op_prefix RD0260 -seq2_op_prefix RE2140

Computes the posterior probabilities of base pairing for each sequence and dumps the probabilities to
RD0260_pp.txt and RE2140_pp.txt files. The content of each file is formatted as a matrix of NxN 
entries where (i,j)'th entry is the linear probability of base pairing for the corresponding sequence.

And;

./PARTS input/RD0260.seq input/RE2140.seq -stochsample -nsamp 1001 -seq1_op_prefix RD0260 -seq2_op_prefix RE2140

Generates 1001 structural alignments and dumps the structures and alignments into RD0260_sampled_cts.ct,
RE2140_sampled_cts.ct, RD0260_RE2140_sampled_alns.aln

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Copyright 2007-2008-2009, Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews.