Integron Finder
Finds integrons in DNA sequences
You can use it in command line, see installation below, or, you can use it online on the Mobyle Webserver (closing end of 2016) and Galaxy Pasteur.
See Documentation for how to use it:
Installation
pip install integron_finder
Licence:
Integron Finder is under open source licence GPLv3
Dependencies :
- Python 2.7
- Pandas 0.18.0
- Numpy 1.9.1
- Biopython 1.65
- Matplotlib 1.4.3
- psutils 2.1.3
- HMMER 3.1b1
- INFERNAL 1.1
- Prodigal V2.6.2
Usage
usage: integron_finder [-h] [--local_max] [--func_annot] [--cpu CPU]
[-dt DISTANCE_THRESH] [--outdir .] [--linear]
[--union_integrases] [--cmsearch CMSEARCH]
[--hmmsearch HMMSEARCH] [--prodigal PRODIGAL]
[--path_func_annot bank_hmm] [--gembase]
[--attc_model file.cm] [--evalue_attc 1]
[--keep_palindromes] [--no_proteins]
[--max_attc_size 200] [--min_attc_size 40]
[--eagle_eyes] [-V]
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_THRESH, --distance_thresh DISTANCE_THRESH
Two elements are aggregated if they are distant of
DISTANCE_THRESH [4kb] or less
--outdir . Set the output directory (default: current)
--linear Consider replicon as linear. If replicon smaller than
20kb, it will be considered as linear
--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 bank_hmm
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
--attc_model file.cm path or file to the attc model (Covariance Matrix)
--evalue_attc 1 set evalue threshold to filter out hits above it
(default: 1)
--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.
--max_attc_size 200 set maximum value fot the attC size (default: 200bp)
--min_attc_size 40 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.
-V, --version show program's version number and exit
Example
integron_finder myfastafile.fst --local_max --func_annot
Output :
A folder name Results_id_genome, inside there are different files :
- *.gbk : contains the input sequence with all integrons and features found.
- *.integrons : contain list of all element detected (attc, protein near attC, integrase, Pc, attI, Pint) with position, strand, evalue, etc...
- *.pdf : representation of complete integrons detected (with integrase (redish) and at least one attc (blueish)). If a protein has a hit with an antibiotic resistance gene, it's yellow, otherwise grey.
and one folder, other
, containing the different outputs of the different steps of the program.
Mobyle and Galaxy
You can use this program without installing it, through two webservers:
- Mobyle (closing end of 2016)
- Galaxy Pasteur
Citation
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.