Mobile Genetic Element Coordinates Extractor (MoGECE) is a program that extracts mobile genetic element location for bacterial and archaeal genomes from outputs created by MGE analysis software. MoGECE then generates files that can be used for viewing that location in genome visualization software.
Version 1.0.2 - May 28, 2018.
Available from https://github.com/danillo-alvarenga/mogece.
MoGECE runs on Python 3.4+ and has been tested on Debian 9 and Ubuntu 16.04. It should work on any modern GNU/Linux distro. No installation for this program is required. However, since it works on outputs from other software, it is necessary to have access to such software in order to be able to use this program adequately.
For convenience, after downloading and extracting the latest MoGECE release from GitHub you can move the extracted directory to the desired destination and add it to your path:
mv GapHelper/ bioinformatics/
cd bioinformatics/GapHelper/
echo 'export PATH=$PATH'$(pwd) >> ~/.bashrc
source ~/.bashrc
Supported MGE analysis outputs in this version include files generated by the programs Alien_Hunter, ISsaga, MinCED, OligoWords, OASIS, PhiSpy, SeqWord Gene Island Sniffer and VirSorter. Currently supported visualization software include Artemis and GView.
MoGECE has been developed with the following program versions in mind:
- Alien_Hunter 1.7
- Artemis 16.0.0
- GView 1.7
- ISsaga 03/09/2016
- MinCED 0.3.0
- OligoWords 1.2
- OASIS 8/11/08
- PhiSpy 2.3
- SeqWord Gene Island Sniffer 1.0
- VirSorter 1.0.3
Note: Older or newer versions of these programs as well as other operating systems might also work, but since they have not been tested this is not guaranteed.
MoGECE.py [-h] [-v] -f File (-l | -i | -m | -o | -w | -p | -s | -r) [-a] [-g]
optional arguments:
-h, --help | show a help message and exit
-v, --version | show version and exit
-f File, --file File | prediction file
-l, --alienhunter | using Alien_Hunter sco prediction file
-i, --issaga | using ISsaga csv prediction file
-m, --minced | using MinCED gff prediction file
-o, --oasis | using OASIS gff prediction file
-w, --oligowords | using OligoWords out prediction file
-p, --phispy | using PhiSpy tbl prediction file
-s, --sniffer | using SeqWordSniffer out prediction file
-r, --virsorter | using VirSorter fasta prediction file
-a, --artemis | generate an Artemis gff file
-g, --gview | generate a GView csv file
In order to run MoGECE, indicate the output file you wish to process, the program in which this output file was created and the program(s) in which you want to visualize the results. Only one file may be processed at each run, but both visualization files may be created at once if you wish.
Example: MoGECE -f Escherichia\_coli\_K12.sco -l -a -g
Note: MoGECE is accompanied by an
Analyses.tar.gzfile containing results for the MGE analyses of 21 publicly available bacterial and archeal genomes to be used as examples. TheAnalyzedGenomes.mdfile included with this program lists the genomes analyzed for that dataset. If you are not interested in examples, you may download the MoGECE.py script separately.
Alien_Hunter generates three files after analysis. One of these files is a .sco file, which indicates coordinates and scores for the predicted genomic islands. Use the sco file as input for MoGECE.
For ISsaga analysis results, it is necessary to first download the xls table containing IS annotations. This table is available in the Annotation Report section and can be downloaded by clicking on annotation > extract annotation > Excel annotation file. Open this file in a spreadsheet editor such as LibreOffice Calc or Microsoft Excel and save it as a .csv file from the file menu. This csv file can then be used as an input for MoGECE. Keep in mind that MoGECE ignores elements tagged as probable false positives by ISsaga.
By default, MinCED outputs results in a tab-separated values table to the terminal. For MoGECE, create a .gff file instead by adding the parameter -gff (not -gffFULL) to its command and pointing a filename for writing.
OASIS analyses produce two files: a .fasta file containing both nucleotide and amino acid sequences and a .gff file containing information about the predicted insertion sequences. Use the gff file as the MoGECE input.
OligoWords writes a .out file for each genome analyzed containing all genomic island results to the output folder inside the software directories. Look for this file and take it for MoGECE processing. MoGECE takes scores from the calculated pattern skew (the n0_4mer:PS results).
After PhiSpy finishes analysis, the output directory will host a file named prophage.tbl pointing the predicted prophages. This is the file that should be fed to MoGECE.
Similarly to OligoWords, Sniffer also creates a .out results file with coordinates and pattern skews that can be used with MoGECE.
VirSorter writes a large number of files during analysis. The relevant coordinates for MoGECE can be found in the headers from fasta sequences written to the Predicted_viral_sequences directory. Instead of running MoGECE on each fasta separately, you may first concatenate the predicted prophage files into a single file.
MoGECE will output either a feature table file for visualization in Artemis (a .ft file), a comma-separated values table for GView (a .csv file), or both according to the parameters you have chosen when running the program.
The files produced will be named according to the program output in which they were based, e.g. an Alien_Hunter output file used as input for MoGECE with the -a and -g parameters will be processed and two files will be created: alienhunter.csv and alienhunter.ft.
When using GView, make sure to add all the processed outputs containing the MGE you wish to visualize to the directory where your target GenBank genome file is stored along with the GViewStyleSheet.gss file included with this software so that GView can recognize them correctly. Select the gb and the gss files in the Open Files window. Beware that if one or more of the supported programs were not used in your pipeline or produced negative results, for this particular style sheet to work you will need to create dummy csv files for them or else GView will not show any output for the results of other programs.
For visualization in Artemis, select file > read an entry in the genome annotation viewer. Change file types to "all files" and add the feature table. You may concatenate different feature tables into a single file so that you can view all results at once.
MoGECE adds scores for files containing such information (Alien_Hunter, OligoWords and SeqWords Gene Island Sniffer outputs). For software where this information is absent, it assumes 1 as the score for every MGE coordinate.
If you find this software useful in your research, please cite the following references according to the programs you use:
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Alvarenga DO, Moreira LM, Chandler M, Varani AM (2018) A practical guide for comparative genomics of mobile genetic elements in prokaryotic genomes. In: Setubal C, Stoye J, Stadler PF (eds) Comparative Genomics. Methods in Molecular Biology, vol. 1704. New York, NY: Humana Press. pp. 213-242. doi: https://doi.org/10.1007/978-1-4939-7463-4_7
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Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 18:2196-2203. doi: https://doi.org/10.1093/bioinformatics/btl369.
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Carver T et al. (2012) Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28:464-469. doi: https://doi.org/10.1093/bioinformatics/btr703.
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Petkau A et al. (2010) Interactive microbial genome visualization with GView. Bioinformatics 26:3125-3126. doi: https://doi.org/10.1093/bioinformatics/btq588.
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Varani AM et al. (2011) ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 12:R30. doi: https://doi.org/10.1186/gb-2011-12-3-r30.
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Angly F, Skennerton C (2015) Mining CRISPRs in Environmental Datasets (MinCED). Available from https://github.com/ctSkennerton/minced.
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Reva ON, Tümmler B (2005) Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 6:251. doi: https://doi.org/10.1186/1471-2105-6-251.
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Robinson DG, Lee MC, Marx CJ (2012) OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences. Nucleic Acids Res 40:e174. doi: https://doi.org/10.1093/nar/gks778.
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Akhter S, Aziz RK, Edwards RA (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 40:e126. doi: https://doi.org/10.1093/nar/gks406.
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Ganesan H et al. (2008) The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9:333. doi: https://doi.org/10.1186/1471-2105-9-333.
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Roux S et al. (2015) VirSorter: mining viral signal from microbial genomic data. PeerJ 3:e985. doi: https://doi.org/10.7717/peerj.985.
If you experience any issues or would like to see support for an additional feature implemented in MoGECE, please file a request in the GitHub issue tracker or email it to the developer. Feel free to contact the developer with any further questions regarding this software. You can reach him at mailto:[email protected].
Copyright © 2016-2018 Danillo Oliveira Alvarenga
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program 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 Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/agpl-3.0.html.
The dataset included with this program is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.