Finds integrons in DNA sequences
You can use it in command line, see installation below, or you can use it online on the Galaxy Pasteur.
See Documentation for how to use it:
Nota Bene: version 2.0 isn't fully released yet. The pip installation below is for the version 1.5 with python2.7. If you want the version 2.0, you can install it with pip, but there are still a few minor bugs around (see issues).
pip install git+https://github.com/gem-pasteur/Integron_Finder/#egg=integron_finder
pip install integron_finder
for more installation options, or for developer installation see documentation
For reproducibility and easy way to use integron_finder without installing third party software (hmmsearch, ...) or libraries, we provide containers based on singularity
So you just have to install singularity (https://github.com/singularityware/singularity)
then
singularity run shub:gem-pasteur/Integron_Finder -h
to run the last version (from master branch) if you prefer download a specific version (with renaming the container on the fly)
singularity pull --name integron_finder shub:gem-pasteur/Integron_Finder:2.0
when you have the image in local you can use it as if integron_finder has been installed
./integron_finder -h
From 2.0 version, Integron_Finder is available as conda package. Integron_finder is in bioconda channel. (The advantage with this solution is that it will install prodigal, hmmer, and infernal too.)
-
install conda
-
Set up channels:
conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda -
install integron_finder:
conda install integron_finder
If you want to develop or submit a patch on this software you are welcome. See Developer installation in documentation.
- Integron Finder is developed and released under open source licence GPLv3 (see COPYING file)
- Resfams is provided with the courtesy of Dantas, Gautam http://www.dantaslab.org/resfams
- The other data files:
- attc_4.cm
- integron_integrase.hmm
- phage-int.hmm
are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License
We encourage contributions, bug report, enhancement ...
But before to do that we encourage to read the contributing guide.
- Python >=3.4
- Pandas >=0.22.0
- Numpy >=1.14.2
- Biopython >=1.70
- Matplotlib >=2.2.2
- HMMER >=3.1b2
- INFERNAL >=1.1.2
- Prodigal >=2.6.2
usage: integron_finder [-h] [--local-max] [--func-annot] [--cpu CPU]
[-dt DISTANCE_THRESHOLD] [--outdir OUTDIR]
[--union-integrases] [--cmsearch CMSEARCH]
[--hmmsearch HMMSEARCH] [--prodigal PRODIGAL]
[--path-func-annot PATH_FUNC_ANNOT] [--gembase]
[--annot-parser ANNOT_PARSER_NAME]
[--attc-model ATTC_MODEL] [--evalue-attc EVALUE_ATTC]
[--calin-threshold CALIN_THRESHOLD]
[--keep-palindromes] [--no-proteins] [--promoter-attI]
[--max-attc-size MAX_ATTC_SIZE]
[--min-attc-size MIN_ATTC_SIZE] [--eagle-eyes] [--pdf]
[--gbk] [--keep-tmp] [--split-results]
[--circ | --linear] [--topology-file TOPOLOGY_FILE]
[-V] [--mute] [-v] [-q]
replicon
positional arguments:
replicon Path to the replicon file (in fasta format), eg :
path/to/file.fst or file.fst
optional arguments:
-h, --help show this help message and exit
--local-max Allows thorough local detection (slower but more
sensitive and do not increase false positive rate).
--func-annot Functional annotation of CDS associated with integrons
HMM files are needed in Func_annot folder.
--cpu CPU Number of CPUs used by INFERNAL and HMMER
-dt DISTANCE_THRESHOLD, --distance-thresh DISTANCE_THRESHOLD
Two elements are aggregated if they are distant of
DISTANCE_THRESH [4000]bp or less
--outdir OUTDIR Set the output directory (default: current)
--union-integrases Instead of taking intersection of hits from Phage_int
profile (Tyr recombinases) and integron_integrase
profile, use the union of the hits
--cmsearch CMSEARCH Complete path to cmsearch if not in PATH. eg:
/usr/local/bin/cmsearch
--hmmsearch HMMSEARCH
Complete path to hmmsearch if not in PATH. eg:
/usr/local/bin/hmmsearch
--prodigal PRODIGAL Complete path to prodigal if not in PATH. eg:
/usr/local/bin/prodigal
--path-func-annot PATH_FUNC_ANNOT
Path to file containing all hmm bank paths (one per
line)
--gembase Use gembase formatted protein file instead of
Prodigal. Folder structure must be preserved
--annot-parser ANNOT_PARSER_NAME
the name of the parser to use to get information from
protein file.
--attc-model ATTC_MODEL
Path or file to the attc model (Covariance Matrix).
--evalue-attc EVALUE_ATTC
Set evalue threshold to filter out hits above it
(default: 1)
--calin-threshold CALIN_THRESHOLD
keep 'CALIN' only if attC sites nuber >= calin-
threshold (default: 2)
--keep-palindromes For a given hit, if the palindromic version is found,
don't remove the one with highest evalue.
--no-proteins Don't annotate CDS and don't find integrase, just look
for attC sites.
--promoter-attI Search also for promoter and attI sites. (default
False)
--max-attc-size MAX_ATTC_SIZE
Set maximum value fot the attC size (default: 200bp)
--min-attc-size MIN_ATTC_SIZE
set minimum value fot the attC size (default: 40bp)
--eagle-eyes Synonym of --local-max. Like a soaring eagle in the
sky, catching rabbits (or attC sites) by surprise.
--circ Set the default topology for replicons to 'circular'
--linear Set the default topology for replicons to 'linear'
--topology-file TOPOLOGY_FILE
The path to a file where the topology for each
replicon is specified.
-V, --version show program's version number and exit
--mute mute the log on stdout.(continue to log on
integron_finder.out)
Output options:
--pdf For each complete integron, a simple graphic of the
region is depicted (in pdf format)
--gbk generate a GenBank file with the sequence annotated
with the same annotations than .integrons file.
--keep-tmp keep intermediate results. This results are stored in
directory named tmp_<replicon id>
--split-results Instead of merging integron results from all replicon
in one file, keep them in separated files.
-v, --verbose Increase verbosity of output (can be cumulative : -vv)
-q, --quiet Decrease verbosity of output (can be cumulative : -qq)
integron_finder --local-max --func-annot mysequences.fst
By default, integron_finder will output 3 files under Results_Integron_Finder_mysequences:
mysequences.integrons: A file with all integrons and their elements detected in all sequences in the input file.mysequences.summary: A summary file with the number and type of integrons per sequence.integron_finder.out: A copy standard output. The stdout can be silenced with the argument --mute
The amount of log in the standard output can be controlled with --verbose for more or --quiet for less, and both are cumulative arguments, eg. -vv or -qq.
Other files can be created on demand:
--gbk: Creates a Genbank files with all the annotations found (present in the .integrons file)--pdf: Creates a simple pdf graphic with complete integrons--keep-tmp: Keep temporary files. See Keep intermediate files for more.
You can use this program without installing it, through the pasteur galaxy webserver instance:
The paper is published in Nucleic Acid Research.
Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha Nucleic Acids Research 2016; doi: 10.1093/nar/gkw319
Please cite also the following articles:
- Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
- Eddy, S.R. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol, 7, e1002195.
- Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
and if you use the function --func_annot which uses Resfams:
- Gibson, M.K., Forsberg, K.J. and Dantas, G. (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J, 9, 207-216.