MANTIS pipeline

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 <>

Publication for Microsatellite Analysis for Normal Tumor InStability

MANTIS IN pipelines

 (14)
2016
PMCID: 5082761
PMID: 27752055
DOI: 10.1038/srep35284

[…] by the institutional animal care and use committee (iacuc) at yale university., detailed protocols for genome and rna sequencing of b. microti isolates are provided in supplemental methods., tandem repeat finder (trf)59 was used to identify all micro-satellites and mini-satellites (mx-satellites) in the reference b. microti r1genome assembly25. in house perl scripts were used to extract unique […]

2015
PMCID: 4502944
PMID: 26173872
DOI: 10.1186/s12864-015-1746-3

[…] positioned within subtelomeric regions, if they were located within the hypervariable var, rifin and stevor families or if they were positioned within repetitive sequences as identified by tandem repeat finder [45]. the dataset was further filtered to exclude isolates with missing calls at >5 % of all positions and snps with calls missing in >10 % of isolates. a total of 85 isolates […]

2015
PMCID: 4526542
PMID: 26244892
DOI: 10.1371/journal.pone.0134897

[…] least 90 amino acids (aa) was selected when no homology could be found with any other known herpesviral genes using blast. detection of the tandem repeats was carried out using the software “tandem repeat finder” [44], using standard settings., the tehv3 genome was compared with that of chelonid herpesvirus 5 (chhv5), the only other available genome of a chelonian herpesvirus [22] using […]

2014
PMCID: 3928620
PMID: 24438474
DOI: 10.1186/1471-2164-15-38

[…] 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 […]

2014
PMCID: 3928620
PMID: 24438474
DOI: 10.1186/1471-2164-15-38

[…] 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 […]

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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