MANTIS specifications

Information


Unique identifier OMICS_20470
Name MANTIS
Alternative name Microsatellite Analysis for Normal Tumor InStability
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format 6-column BED format
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements NumPy, Pysam
Maintained Yes

Subtool


  • Repeat Finder

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Documentation


Maintainer


  • person_outline Sameek Roychowdhury <>

MANTIS article

MANTIS citations

 (3)
2015
PMCID: 4598586

[…] gene and te annotations were obtained from brad (http://brassicadb.org/brad/). tandem and inverted repeats were detected using tandem repeat finder and inverted repeat finder software packages following default parameters (benson, 1999; warburton et al., 2004)., to remove the influence of nucleotide variations during the calling […]

2014
PMCID: 3928620

[…] respectively, were predicted based on transposon database using softwares of repeatmasker and repeatproteinmask (http://www.repeatmasker.org/). tandem repeat sequences were predicted by using tandem repeat finder (http://tandem.bu.edu/trf/trf.html). prophage islands were predicted using prohinder software and aclame database (http://aclame.ulb.ac.be/), thereafter we performed blast comparison […]

2011
PMCID: 3096633

[…] of h. parasuis strain sh0165 (cp001321) using blastn (minimum sequence identity of 95% and expected threshold of 1e−5). short dna repeats in the genome sequences were searched with a perl script repeat_finder (http://folk.uio.no/stephanf/repeat_finder.html) and graphical representations of the patterns in sequence conservation were created using weblogo [19]. protein transmembrane helices […]

MANTIS institution(s)
Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA; Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
MANTIS funding source(s)
Supported by American Cancer Society [grant number MRSG-12-194-01-TBG]; the Prostate Cancer Foundation; the National Human Genome Research Institute [grant number UM1HG006508]; the National Cancer Institute [grant number UH2CA202971]; the American Lung Association; Pelotonia; and Fore Cancer Research.

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