MaxEntScan protocols

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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 in pipelines

 (4)
2017
PMCID: 5440144
PMID: 28514307
DOI: 10.1097/MD.0000000000006914

[…] aggregation consortium; the benign variants, including synonymous, harmless missense predicted by polyphen-2 (cambridge, ma) and sift software, and those predicted to have no impact on splicing by maxentscan (cambridge, ma). subsequently, clinical symptoms of developmental delay, ophthalmic diseases, and microcephaly subsequently served as filtering indexes to analyze the candidate variants. […]

2016
PMCID: 4901439
PMID: 27287018
DOI: 10.1186/s13059-016-0990-4

[…] were classified as se, mxe, ri, alternative donor site (a5ss), or alternative acceptor site (a3ss). 3′ss and 5′ss strengths of the differentially spliced exons and introns were calculated using the maxentscan approach []., all statistical analyses were executed using r []. figures were built using r [], cytoscape [], circos plot [], sashimi plot [], and inkscape []., additional file 1: […]

2016
PMCID: 5366069
PMID: 27884935
DOI: 10.1136/jmedgenet-2016-104215

[…] each variant was given a custom deleterious score based on a six-point scale, calculated using output from annovar. variants predicted to affect splicing were assigned a deleterious score based on maxentscan score differences, and the relationship of variants present in known disease-causing genes analysed for pathogenicity using clinvar. variants with minor allele frequency (maf) >1% […]

2015
PMCID: 4376664
PMID: 25714049
DOI: 10.1038/nn.3975

[…] order, were retained as candidates supporting head-to-tail junction. the strength of potential splicing sites supported by these candidate head-to-tail junction reads was then estimated using maxentscan . the exact junction site was determined by selecting the donor and accepter sites with the highest splicing strength score. candidate circrnas were reported if the head-to-tail junction […]


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MaxEntScan in publications

 (172)
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] 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 […]

PMCID: 5948732
PMID: 29751740
DOI: 10.1186/s12881-018-0590-0

[…] 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 […]

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

[…] was defined as a potential nmd target if its accumulative abundance increased more than twofold in 725ri-1 rice compared to wt plants, with a p value smaller than 0.05, determined by cuffdiff []., 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 […]

PMCID: 5933811
PMID: 29684050
DOI: 10.1371/journal.pgen.1007360

[…] 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 […]

PMCID: 5924558
PMID: 29673180
DOI: 10.3390/genes9040216

[…] 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 […]


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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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