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Protocols

ESEfinder specifications

Information


Unique identifier OMICS_09613
Name ESEfinder
Interface Web user interface
Restrictions to use None
Input data Sequences
Input format FASTA
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Publications for ESEfinder

ESEfinder citations

 (238)
library_books

Incorporating epilepsy genetics into clinical practice: a 360°evaluation

2018
PMCID: 5945675
PMID: 29760947
DOI: 10.1038/s41525-018-0052-9

[…] diction tools—predictions on protein level were obtained from dbNSFP Functional Predictions and Cores 3.0 database while the variants were submitted to bioinfomatic software tools, e.g., NNSplice and ESEfinder for predictions on transcriptional level. The ACMG guidelines were applied to the resulting variants. Pathogenic variants are listed in Table : SCN8A (n = 4) and SCN2A (n = 3) were the two m […]

library_books

Genetic variants of ALDH2 rs671 and CYP2E1 rs2031920 contributed to risk of hepatocellular carcinoma susceptibility in a Chinese population

2018
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105

[…] its silencing or inhibiting effects, ESS recruits many proteins that negatively affect the splicing mechanism.Prediction results of changing splicing regulation were also determined with four tools: ESEfinder, ESRSearchi, PESX, and RESCUE_ESE. Abnormal splicing changes are thought to contribute to cancer onset and progression.– These splicing changes induce a nonsynonymous mutation at the rs671 s […]

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

[…] oftware (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html) [], the BerkeleyDrosophila Genome Project (BDGP) splice prediction tool (http://www.fruitfly.org/seq_tools/splice.html) [] and ESEFinder 3.0 software (http://rulai.cshl.edu) []. […]

call_split

Combining targeted panel based resequencing and copy number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

2018
Sci Rep
PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1
call_split See protocol

[…] AN); v) non-canonical splicing variants in silico predicted to cause a deleterious effect by several splicing tools (Human Splicing Finder, MaxEntScan, Splice Site Finder-like, NNSPLICE, GeneSplicer, ESEFinder); vi) genes associated with the most likely clinical phenotype in each case. Alamut software (Interactive Biosoftware, Rouen, France) was used to infer in silico predictions of variant patho […]

library_books

A Comprehensive in Silico Analysis of Regulatory SNPs of Human CLEC7A Gene and Its Validation as Genotypic and Phenotypic Disease Marker in Recurrent Vulvovaginal Infections

2018
PMCID: 5869923
PMID: 29616193
DOI: 10.3389/fcimb.2018.00065

[…] e selection of functional SNPs. FuncPred, the main tool of SNPinfo is composite of different singleton tools including SNP3D, rescue ESE, MATCH, miRanda, Polyphen, TRANSFAC12.1, miRBase, FAS–ESS, and ESEfinder (Xu and Taylor, ). RegulomeDB divides functional SNPs into six different classes ranging from C1 to C6. Class 1 SNPs mostly include expression and binding signals, with six subclasses from 1 […]

library_books

Coordinated expression and genetic polymorphisms in Grainyhead like genes in human non melanoma skin cancers

2018
BMC Cancer
PMCID: 5755140
PMID: 29301499
DOI: 10.1186/s12885-017-3943-8

[…] ript. We employed two algorithms to search for exonic splicing enhancers (ESE). RESCUE-ESE [] did not detect any potential ESEs that would overlap with the location of SNP rs141193530 or rs151326764. ESEfinder3.0 [] predicted some changes in binding of serine and arginine rich splicing factors (SRSF) to the region containing SNP rs141193530, which were: loss of one SRSF5 potential binding site and […]

Citations

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ESEfinder institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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