Menu
▾
▴
Home
RAFTS3: Rapid Alignment Free Tool for Sequences Similarity Search
RAFST3 is available for Linux 64 bits and Windows 64 bits as standalone application (MCR required, see INSTALLATION). To use of functions in Matlab, Bioinformatics Toolbox and Mex compiler are needed.
Copyright © 2013 Ricardo A. Vialle, Fábio O. Pedrosa, Vinicius A. Weiss, Dieval Guizelini, Juliana H. Tibaes, Jeroniza N. Marchaukoski, Emanuel M. de Souza and Roberto T. Raittz. All rights reserved.
Please report bugs, problems and enlightments to ricardovialle@gmail.com.
1. Introduction
RAFTS3 can perform high-speed protein search comparisons locally using a desktop computer or laptop. RAFTS3 performed searches much time faster than those with BLASTp against large protein databases such as NR and Pfam, with a small loss of sensitivity depending on the similarity degree of the sequences. RAFTS3 is a new alternative for fast comparison of protein sequences, genome annotation and biological data mining.
RAFTS3 utilizes a filter step for candidate selection based on shared k-mers and a comparison measure using a binary matrix of co-occurrence of amino acid residues.
2. Installation
2.1. Requirements
Before downloading and installing RAFTS3, make sure that your computer or server fulfills the following requirements:
- UNIX or Windows platform;
- MCR (MATLAB Component Runtime).
2.1.1. MCR (MATLAB Component Runtime)
RAFTS3 requires the MATLAB Component Runtime to run. It can be found to download in RAFTS3 project on SourceForge page https://sourceforge.net/projects/rafts3/files/. To install MCR follow these steps for chosen platform:
For Linux:
- Extract and install MCR (MATLAB Component Runtime):
tar -xvzf MCR_LINUX64b.tar
cd MCR_LINUX64b
./installMCR.sh <mcr absolute="" destination="" path=""></mcr>
For Windows:
- Extract and install MCR (MATLAB Component Runtime):
- Unzip MCR_WIN64b.zip
- Double click at MCR_WIN64b.exe
- Follow installation instructions
- Add the installed folder to environment variable PATH "yourpath\MATLAB Compiler Runtime\v717\runtime\win64"
- Restart your computer
2.2. Downloading RAFTS3
RAFTS3 is available at https://sourceforge.net/projects/rafts3/files/. After downloading the file, follow instructions below.
For Linux:
- Extract RAFTS3:
tar -xvzf RAFTS3_LINUX64b.tar.gz
cd RAFTS3_LINUX64b
- Add execution permission for files:
chmod u+x run_makerafts3db.sh makerafts3db run_rafts3.sh rafts3 run_rafts3x.sh rafts3x
For Windows:
- Unzip RAFTS3_WIN64b.zip
3. RAFTS3 usage
To perform searches against a database, first is needed run a database formatting process. Use the MAKERAFTS3DB for it.
3.1. MAKERAFTS3DB
MAKERAFTS3DB uses a multi-fasta file as input, for example the NCBI NR database. To run follow instructions bellow:
For Linux:
./run_makerafts3db.sh <MCR installation folder> database [-num_inds int_value]
[-kmer_size int_value] [-limit int_value] [-out output_file]
For Windows:
makerafts3db.exe database [-num_inds int_value] [-kmer_size int_value]
[-limit int_value] [-out output_file]
3.1.1 MAKERAFTS3DB parameters
Below are the description of each available parameter for MAKERAFTS3DB.
| Parameter | Description |
|---|---|
| database | is the database, a fasta or multi-fasta formatted file with protein sequences. |
| -num_inds | specifies the number of k-mers randomly selected per sequence. Default is 10. |
| -kmer_size | is the length k of the k-mer. Default is 6. |
| -limit | is the length of the sequence used to select the k-mers. Default is 120. |
| -out | specifies output files names pattern. Default is <file_in>.mat</file_in> |
3.2. RAFTS3
RAFTS3 searches protein sequences against a formatted database. To run follow instructions bellow:
For Linux:
./run_rafts3.sh <MCR installation folder> input_file makerafts3db_file
[-num_correlation int_value] [-max_target_seqs int_value]
[-num_alignments int_value] [-out output_file] [-outfmt format]
[-max_headers_length int_value]
For Windows:
rafts3.exe input_file makerafts3db_file [-num_correlation int_value]
[-max_target_seqs int_value] [-num_alignments int_value] [-out output_file]
[-outfmt format] [-max_headers_length int_value]
3.2.1 RAFTS3 parameters
Below are the description of each available parameter for RAFTS3.
| Parameter | Description |
|---|---|
| input_file | is a fasta or multi-fasta formatted file with protein sequences. |
| makerafts3db_file | is the .mat file created with makerafts3db. |
| -max_target_seqs | specifies how many hits are shown for each query. The default is 1. |
| -num_correlation | specifies for each hit, how many BCOMs correlation are calculated.The default is 50. |
| -num_alignments | how many Smith-Waterman alignments are made for hits found. The default is 1. |
| -out | specifies output file name. Default is rafts3_output.txt. If 'stdout' specified, results are printed into screen. |
| -outfmt | specifies output formatting options. Options available are 'blast-like' and 'rafts3'. Default is 'blast-like'. |
| -max_headers_length | specifies the maximum length of query and subject header shown. Default is 22. |
3.2.2 RAFTS3 output
Two output format are available for RAFTS3, 'blast-like' and 'rafts3'. Each one is explained below.
blast-like - The output information is like the Blast tabular output with alignment information. Each column containing information:
Query
Subject
Identity
Align length
Mismatches
Gap Opening
Query Start Position
Query End Position
Subject Start Position
Subject End Position
E-Value
BitScore
Query Coverage
Subject Coverage
Smith-Waterman Score
Relative Score
BCOM score
BCOM correlation
rafts3 - Tabular output format without alignment information, with each column containing:
Query
Subject
BCOM score
BCOM correlation
3.3. RAFTS3X
RAFTS3X performs search on a protein database using a translated nucleotide query. Its parameters and outputs are the same of regular RAFTS3 for protein sequences.
3.4. Instructions for use of functions in MatLab
In order to perform searches against a protein sequences database, the function 'makerafts3db.m' need to be executed. The returned structure is needed to perform the searches using the function 'rafts3.m' for protein query sequence or 'rafts3x.m' for translated nucleotide query. The formated structure can be used as function parameter for searches, avoiding loading. Mex files are compiled from .c files during first
execution.
For more information about each function and their parameters try help.
4. Troubleshooting
If you experience some problems with mcc-generated shell script on Linux please try setting the LD_LIBRARY_PATH environment variable to let the system know where to find Matlab Compiler Runtime library. To do this, cut-and-paste mycsh and/or mybash instructions below into your respective .cshrc or .bashrc file in your home directory. Dont forget to source .cshrc or source .bashrc at the csh or bash system prompt if you want it effective immediately in the current shell. After that you can execute applications directly from executable files, without specify the MCR path.
#insert the following to your .cshrc file
#source .cshrc to make the additions effective for current session
#points to system default version of matlab
set MCRROOT=<MCR installation folder>
set LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64
set MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client
set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}
setenv XAPPLRESDIR ${MCRROOT}/X11/app-defaults
# insert the following to your .bashrc file
# source .bashrc to make the additions effective for current session
# points to system default version of matlab
MCRROOT=<MCR installation folder>
LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
export LD_LIBRARY_PATH;
export XAPPLRESDIR;
5. License
IMPORTANT! READ CAREFULLY: THIS IS A LEGAL AGREEMENT
RAFTS3: Rapid Alignment Free Tool for Sequences Similarity Search software Copyright © 2013 Ricardo A. Vialle, Fábio O. Pedrosa, Vinicius A. Weiss, Dieval Guizelini, Juliana H. Tibaes, Jeroniza N. Marchaukoski, Emanuel M. de Souza and Roberto T. Raittz. All rights reserved.
RAFTS3 software development: Ricardo A. Vialle*, Fábio O. Pedrosa**, Vinicius A. Weiss**, Dieval Guizelini*, Juliana H. Tibaes*, Jeroniza N. Marchaukoski*, Emanuel M. de Souza** and Roberto T. Raittz*
* Laboratory of Bioinformatics
Federal University of Parana
Department of Technological Education
Rua Dr. Alcides Vieira Arcoverde, 1225, Jardim das Américas
Curitiba – PR
Brazil
** Graduate Program in Science-Biochemistry
Federal University of Parana
Department of Biological Sciences
Avenida Coronel Francisco Heráclito dos Santos, 210, Jardim das Américas
Curitiba – PR
Brazil
The RAFTS3 software is only available for download from https://sourceforge.net/projects/rafts3/
By installing RAFTS3, you are agreeing to be bound by this agreement ("Agreement"). If you do not agree with all of the terms of this Agreement, reject the Agreement by refusing to install the RAFTS3 software.
1) Definitions
1.1) "DEVs" means the developers and copyright owners of RAFTS3 software, as defined at the beginning of this License Agreement.
1.2) "Software" means all software and materials provided to you by DEVs as part of the RAFTS3 program, excluding the MATLAB Compiler Runtime (MCR).
2) Ownership
2.1) The Software is owned and copyrighted by DEVs. The MATLAB Compiler Runtime (MCR) is provided royalty-free with the MATLAB Compiler by The MathWorks, Inc. ("MathWorks"), and is redistributed by DEVs subject to the terms of a license agreement between DEVs and MathWorks. You may not directly or indirectly sell, lease, rent, redistribute, license, sublicense, lend, give, or transfer the MATLAB Compiler Runtime (MCR). This Agreement confers no title or ownership in the Software and is not a sale of any rights in the Software.
2.2) This Agreement does not grant you and/or any person(s) acting with you or for you, any rights or license with respect to the source code of the Software.
3) Disclaimer of Warranties & Limitation of Liability
THE SOFTWARE AND THE MATLAB COMPILER RUNTIME (MCR) ARE PROVIDED BY DEVs "AS IS" WITHOUT A WARRANTY OF ANY KIND, AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL DEVs BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE AND THE MATLAB COMPILER RUNTIME (MCR), EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. NO WARRANTY IS MADE THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS.
4) Indemnification
You agree to fully indemnify and hold harmless DEVs from and against any and all claims, liabilities, demands, suits, losses, damages, costs, settlement amounts, and/or expenses, including but not limited to attorneys' fees, arising out of your use of the Software.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The Software uses, with or without modifications, some custom MATLAB functions ("custom functions") submitted by their copyright owners, and under the BSD LICENSE, to The MathWorks File Exchange repository; these custom functions are:
- onbits, Copyright (c) 2008, James Tursa. All rights reserved.
- prcorr2, Copyright (c) 2001-2002, Peter Rydesäter. All rights reserved.
The following BSD LICENSE applies to these custom functions only, referred to as "THIS SOFTWARE":
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.