The directory 'deepBlockAlign_v*' contains following programs and datasets

1. deepBlockAlign.x: program to align two or more RNA-seq read block profiles
2. deepBlockAlign.c: source code of deepBlockAlign
3. plotdeepBlockAlign.pl: wrapper program to deepBlockAlign. Also output alignments in graphical format
4. plotblockAlign.r: accessory R program to plotdeepBlockAlign.pl
5. test_suite/human_eb.blockGroups: Benchmark dataset used in current study

To install deepBlockAlign, download deepBlockAlign.tar.gz and unpack it

tar -zxvf deepBlockAlign.tar.gz
A directory, deepBlockAlign will be created, now execute

make or make all
which compiles deepBlockAlign and creates an executable

deepBlockAlign.x

deepBlockAlign.x -q <query file> -s <subject file> [ARGUMENTS]

==========================================================
                     DeepBlockAlign
a tool for aligning RNA-seq profiles of read block patterns
==========================================================

usage: deepBlockAlign.x -q <file> -s <file> [ARGUMENTS]

[INPUT]
 -q  <file>   query file (blockbuster output)
 -s  <file>   subject file (blockbuster output)

[ARGUMENTS: Block Group Alignment]
 -d  <double> distance weight (default: 6.0)
 -b  <double> block similarity weight (default: 1.0)
 -g  <double> gap penalty (default: -1.0)
 -a  <int>    print alignment 1=on (default: 0)
 -l  <file>   create file containing alignment score of all blocks against all blocks
 -f  <file>   create file necessary to plot block group alignment
 -p  <int>    only align pairs of block groups e.g 1 with 1, 2 with 2 etc (default:0)

[ARGUMENTS: Block Alignment]
 -c  <int>    gap initialization penalty (default: -2)
 -e  <int>    gap extension penalty for (default: -1)
 -t  <double> threshold for expression difference between two blocks (default: 1.0)
 -m  <int>    match score (default: 1)
 -n  <int>    mismatch score (default: -1)
 -z  <int>    profile shape difference penalty (default: 1)
 -h           this helpful message

[VERSION]
 v1.3 (Oct 15, 2014)

plotdeepBlockAlign.pl -i <query file> -j <subject file>

Program: plotdeepBlockAlign.pl (align and visualize the alignment of read profiles)
Author: University of Copenhagen, Denmark
Version: 1.0
Contact: sachin@rth.dk
Usage: plotdeepBlockAlign.pl -i <file> -j <file> [OPTIONS]
 -i <file>     [first block group file]
 -j <file>     [second block group file]
 -f <id>       [first block group id]
 -s <id>       [second block group id]
 -p <dir>      [directory with programs (deepblockalign.x etc)]
 -o <dir>      [directory with output files]
 -x <string>   [prefix for temporary files, useful when running on queue]
 -l            [output in HTML format]
 -a <string>   [path to hyperlink alignment images from the HTML format]
 -q            [output in plain text format]
 -k            [keep the block and block group alignment files]
 -v <string>   [first block group title (default: first)]
 -w <string>   [second block group title (default: second)]
[OPTIONS: Block Group Alignment]
 -d <double>   [distance weight (default: 1.0)]
 -b <double>   [block similarity weight (default: 1.0)]
 -g <double>   [gap penalty (default: -1.0)]
[OPTIONS: Block Alignment]
 -c  <int>     [gap initialization penalty (default: -2)]
 -e  <int>     [gap extension penalty (default: -1)]
 -t  <double>  [threshold for expression difference between two blocks (default: 1.0)]
 -m  <int>     [match score (default: 1)]
 -n  <int>     [mismatch score (default: -1)]
 -z  <int>     [profile shape difference penalty (default: 1)]

$./deepBlockAlign.x -q testsuite/snoRNA-HACA-E3.example -s testsuite/hsa-mir-9-1.example
# deepBlockAlign.x v1.3 started at Thu Dec  4 16:25:12 2014
# query: testsuite/snoRNA-HACA-E3.example
# subject: testsuite/hsa-mir-9-1.example
# parameters (block group alignment)
#  distance weight: 1.0; block similarity weight: 1.0; gap penalty: -1.0
# parameters (block alignment)
#  match: 1; mismatch: -1; threshold: 1; shape difference penalty: 1
#  gap penalty (initialization): -2; gap penalty (extension): -1
>cluster_929|E3|chr3:187987781-187987842(+)   >cluster_30|hsa-mir-9-1|chr1:154656768-154656831(-) 0.554014

$./plotdeepBlockAlign.pl -i testsuite/human_eb.blockGroups -j testsuite/human_eb.blockGroups \
-f cluster_176 -s cluster_531 -p .
# plotdeepBlockAlign started at Thu, 04 Dec 2014 16:27:37 +0100
# first block group: cluster_176
# first file: testsuite/human_eb.blockGroups
# second block group: cluster_531
# second file: testsuite/human_eb.blockGroups
computing alignment....done (score: 0.72)
aligning blocks...done
aligning block groups...lsdone (cluster_176_n-a--cluster_531_hsa-mir-424.pdf)
creating final output file...
done (./cluster_176_n-a--cluster_531_hsa-mir-424_FINAL.pdf)

>cluster_929   chr3   187987781   187987842   +   306.50   194   2   E3   snoRNA   Intron

chr3   187987783   187987809   morin_EB_685629   0.500000   +   1
chr3   187987783   187987806   morin_EB_685761   0.500000   +   1
.
.
.
chr3   187987783   187987806   morin_EB_685630   0.500000   +   1

>cluster_929   chr3   187987781   187987842   +   306.50   194   2

For details, please refer to

    1. deepBlockAlign publication
    2. blockbuster publication

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