MaxEntScan statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MaxEntScan
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Tool usage distribution map

This map represents all the scientific publications referring to MaxEntScan per scientific context
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Protocols

MaxEntScan specifications

Information


Unique identifier OMICS_09611
Name MaxEntScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Single/multiple sequences
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yeo Gene

Information


Unique identifier OMICS_09611
Name MaxEntScan
Interface Web user interface
Restrictions to use None
Input data Single/multiple sequences
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yeo Gene

Publication for MaxEntScan

MaxEntScan citations

 (189)
library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] the cbioportal. Effect of splice mutations was predicted on the major transcript with the Alamut Visual Software (Interactive Software, Rouen, France), which contains the algorithms SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder, ESE-Finder, and RESCUE-ESE. Mutation data from all TCGA series were retrieved from the GDC portal in day 29th of September 2017. Frequencies o […]

call_split

Next generation sequencing reveals a new mutation in the LTBP2 gene associated with microspherophakia in a Spanish family

2018
BMC Med Genet
PMCID: 5948732
PMID: 29751740
DOI: 10.1186/s12881-018-0590-0
call_split See protocol

[…] he functional impact of the genomic variations found in the present study, we used the ALAMUT® VISUAL software. This software uses the following relevant prediction tools: i) Splice Site Finder-like, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder and ESE for splicing prediction ii) Align GVGD, SIFT, MutationTaster, PolyPhen-2 and KD4v for missense prediction.To check all the variants det […]

library_books

Position specific intron retention is mediated by the histone methyltransferase SDG725

2018
BMC Biol
PMCID: 5925840
PMID: 29706137
DOI: 10.1186/s12915-018-0513-8

[…] MaxEntScan [] was used to calculate maximum entropy scores for 9 bp spanning the 5′ (donor) splice sites (3 bp in the exon and 6 bp in the intron) and 23 bp spanning the 3′ (acceptor) splice sites (20 […]

call_split

Intronic PAH gene mutations cause a splicing defect by a novel mechanism involving U1snRNP binding downstream of the 5’ splice site

2018
PLoS Genet
PMCID: 5933811
PMID: 29684050
DOI: 10.1371/journal.pgen.1007360
call_split See protocol

[…] effect of the variants on the splice site strengths and the presence of putative splicing regulatory elements were predcited using the Human Splicig Finder (HSF) program (http://www.umd.be/HSF3/) [], MaxEntScan software (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html) [], the BerkeleyDrosophila Genome Project (BDGP) splice prediction tool (http://www.fruitfly.org/seq_tools/splice.h […]

library_books

Accurate Classification of NF1 Gene Variants in 84 Italian Patients with Neurofibromatosis Type 1

2018
Genes
PMCID: 5924558
PMID: 29673180
DOI: 10.3390/genes9040216

[…] ing Module of the variant interpreter software program, Alamut® Visual (Interactive Biosoftware, Rouen, France) with the SpliceSiteFinder (http://www.genet.sickkids.on.ca/~ali/splicesitefinder.html), MaxEntScan (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html), NNSplice (http://www.fruitfly.org/seq_tools/splice.html) and GeneSplicer (http://www.cbcb.umd.edu/software/GeneSplicer/gene […]

call_split

Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early onset/familial prostate cancer

2018
PLoS Genet
PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355
call_split See protocol

[…] ional consequence of truncating/deleterious variants, MutationTaster [] and Uniprot [] were queried. To infer the putative impact on splicing, the splice site predictors Human Splicing Finder 3.0 [], MaxEntScan [], NNSPLICE [] and NetGene2 [] were used. To predict the biological impact of missense mutations, we looked at data from the predictor tools embedded in the NGS Interpretative Workbench fr […]


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MaxEntScan institution(s)
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA, USA

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