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MGEScan specifications

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Unique identifier OMICS_11425
Name MGEScan
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable

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Unique identifier OMICS_11425
Name MGEScan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_11425
Name MGEScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Publications for MGEScan

MGEScan citations

 (8)
library_books

sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII

2017
PMCID: 5389150
PMID: 28403818
DOI: 10.1186/s12864-017-3688-4

[…] that promote non-canonical retrotransposon silencing in this medically relevant fungus., retrotransposon mining with ltr_finder v1.0.6 [], ltr_harvest v1.5.7 [], ltr_struc v1.1 [], ltr_seq [], mgescan v2 [], and transposon_psi (http://transposonpsi.sourceforge.net) programs were used in c. gattii genomes with default parameters. the 17 c. gattii genomes (table ) from vgi, vgii, vgiii, […]

library_books

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

2017
PMCID: 5427498
PMID: 28235826
DOI: 10.1534/g3.116.038638

[…] tes, including ltr retrotransposons, non-ltr retrotransposons, and dna transposons, were de novo identified in the pa42 reference genome, respectively. two computer softwares, ltrharvest () and mgescan (), were used to identify all potential intact ltr retrotransposons. we further filter the candidate ltr tes based on similarity (>80%) and the lengths (>80 bp), as well as the presence […]

library_books

Low diversity, activity, and density of transposable elements in five avian genomes

2017
PMCID: 5486457
PMID: 28190211
DOI: 10.1007/s10142-017-0545-0

[…] of these five avian species (budgerigar, chicken, medium ground finch, turkey, and zebra finch) by using repeatmasker (http://repeatmasker.org) and multiple de novo repeat prediction pipelines (mgescan-non-ltr, ltrharvest, retrotector) (sperber et al. ; ellinghaus et al. ; rho and tang ). by integrating analyses of these five avian species, we can perform a comprehensive analysis of te […]

library_books

Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex

2017
PMCID: 5381639
PMID: 28057730
DOI: 10.1093/gbe/evw302

[…] non-ltr retrotransposons, and dna transposons, were identified separately., two computer software were used here to search for all potential full-length ltr retrotransposons: ltrharvest () and mgescan-ltr (). a previous comparison of various de novo ltr-element identification programs has suggested that these two programs give the best results related to the number of true detected ltr […]

library_books

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

2016
PMCID: 5217101
PMID: 27852011
DOI: 10.1534/g3.116.035923

[…] using bwa-mem ()., long terminal repeat (ltr) retrotransposons were identified in the gallus_gallus-5.0 assembly with an iterative pipeline locatr () that incorporates ltr_struc (), ltr harvest (), mgescan_ltr (), and repeatmasker () search algorithms. these data were compared to a recent ltr annotation of the gallus_gallus-4.0 assembly ()., to call snps and indels for both assemblies, […]

library_books

A new look at the LTR retrotransposon content of the chicken genome

2016
PMCID: 5006616
PMID: 27577548
DOI: 10.1186/s12864-016-3043-1

[…] evidence for internal motifs has been identified. locatr facilitates analysis with four, independently run, structural identification methods: ltr_struc [], ltr harvest [], retrotector [] and mgescan_ltr []. whilst the underlying identification rationales are related, the programs have been previously found to identify markedly different subsets of ltr retrotransposons [–]. differences […]


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MGEScan institution(s)
School of Informatics and Computing, Indiana University, Bloomington, IN, USA; Department of Computer Science and Engineering, Ewha Womans University, Seoul, Korea; Department of Computer Science and Engineering, Hanyang University, Seoul, Korea; Department of Software Convergence Technology, Ajou University, Suwon, Korea
MGEScan funding source(s)
This work was supported by National Research Foundation of Korea grants funded by the Ministry of Education (No. NRF-2015R1D1A1A01059557), by the Korean government (MSIP) (No. KW-2014PPD0053 and No. NRF-2015R1C1A1A01054305), by the National Science Foundation grant (No. DBI-1262588) and by Marine Biotechnology Program (No. PJT200620) of Ministry of Oceans and Fisheries.

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