ADOMA

Alternative display of multiple alignment

About

ADOMA first creates a multiple sequence alignment with ClustalW. ADOMA takes this multiple sequence alignment and converts it to a couple of different files:

- ClustalW alignment file in HTML [default]  
- Simplified alignment file in HTML [default]  
- Colored ClustalW alignment file in HTML   
- Simplified alignment file in txt

The simplified alignment is an alignment were mismatches between sequences can be identified a lot easier. When aligning homologous sequences for example this can be very difficult with a default ClustalW alignment. The simplified alignment displays the parent (or upper) sequence and for all the other sequences it displays a "-" when there is a match between the sequence and the parent sequence, the nucleic or amino acid when there is a mismatch and a "*" when there is a deletion. For an example of the simplified alignment, check the folder Examples and choose one of the simplified HTML files

The colored ClustalW alignment gives nucleic or amino acids a color depending on the nucleic or amino acid and the alignment consensus. The same color code is used as in ClustalX: coloring scheme ClustalX

As input ADOMA requires the fasta files of the sequences that need to be aligned to each other. This can also be a multiple fasta file, but this not neccessary. Also, a prefix for the output files needs to be assigned. The parameters that can be assigned at input are:

-p          For defining the prefix of the output files (mandatory)
-i          The input files in fasta format (mandatory)
-dna        Type of input sequences is DNA [default]
-prot       Type of input sequences is protein
-txt        Create txt output for simplified alignment
-color      Created colored html output for the ClustalW alignment
-clustalw   ClustalW options can be defined here

For more details about parameters, examples of the different output files, etc. check the manual: Manual.pdf

Requirements

ADOMA must be executed in a unix command line.

ADOMA needs ClustalW (version 2.1) to create a multiple sequence aligment from the input sequences. For installation check: http://www.clustal.org/clustal2/

ADOMA needs python (version 2.7 or higher) to create the different displays of the alignment. For installation check: https://www.python.org/downloads/source/

For display of the alignment files in html a internet browser is needed (Google Chrome, Mozilla Firefox, Internet Explorer, etc.). For display of the txt file a text editor is needed.

Installation

ADOMA does not need to be installed. Only the download must be unpacked: tar -zxvf adoma-[version].tar.gz

After unpacking, these files are in the folder adoma-[version]:

- adoma.sh
- convert_aln.py
- README.txt
- LICENSE.txt
- Manual.pdf
- folder: Examples
- folder: Test_data

Usage

For the help file:
./adoma.sh -h
./adoma.sh --help

For executing ADOMA with one multiple fasta file (1):
./adoma.sh -p [PREFIX] -i [sequences.fa]

For example:
./adoma.sh -p Data_1 -i Data_1.fa

(1) This must be a fasta file with more than one sequence (also called: multiple fasta file). Otherwise the alignment can not be created.

It is also possible to put more than one fasta file into ADOMA. These will be merged together for the multiple sequence alignment. To execute ADOMA for multiple fasta files use:
./adoma.sh -p [PREFIX] -i [sequence1.fa] [sequence2.fa]

To test the program there is also some testdata available in the folder Test_data. One example on how to run ADOMA with the test data: ./adoma.sh -p ADOMA_DNA -i Test_data/DNA.fa -dna -txt

For examples with more parameters and the test data, check the manual that is included in the adoma-[version] folder: Manual.pdf

Copyright and license

Copyright (C) 2014 Dionne Zaal

ADOMA 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.

ADOMA 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 ADOMA. If not, see http://www.gnu.org/licenses/