CRYP-SKIP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CRYP-SKIP
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Tool usage distribution map

This map represents all the scientific publications referring to CRYP-SKIP per scientific context
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Associated diseases

This word cloud represents CRYP-SKIP usage per disease context
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Popular tool citations

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Protocols

CRYP-SKIP specifications

Information


Unique identifier OMICS_09621
Name CRYP-SKIP
Interface Web user interface
Restrictions to use None
Input data Single/multiple sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Igor Vořechovský

Publications for CRYP-SKIP

CRYP-SKIP citations

 (10)
library_books

Identification of Two Novel LAMA2 Mutations in a Chinese Patient with Congenital Muscular Dystrophy

2018
Front Genet
PMCID: 5816747
PMID: 29487616
DOI: 10.3389/fgene.2018.00043

[…] 1782+2T > G) is located at the exon–intron boundary, a potential splicing donor site. Therefore, in silico splicing analysis of this variation was performed by using two different web-based programs, CRYP-SKIP and Berkeley Drosophila Genome Project (BDGP). Mutations in splicing sites generally lead to exon skipping or activation of cryptic splice sites. The CRYP-SKIP analysis showed that the point […]

call_split

Activation of a cryptic 5′ splice site reverses the impact of pathogenic splice site mutations in the spinal muscular atrophy gene

2017
Nucleic Acids Res
PMCID: 5716214
PMID: 28981879
DOI: 10.1093/nar/gkx824
call_split See protocol

[…] gorithm (http://genes.mit.edu/cgi-bin/Xmaxentscan_scoreseq.pl) (). The 5′ splice sites were also scored using the HBond score web interface, version 3.4 (http://www2.hhu.de/rna/html/hbond_score.php). CRYP-SKIP prediction algorithm was used to determine whether a splicing mutation of interest would result in exon skipping or activation of cryptic/di novo splice sites (). […]

call_split

Analysis of 31 year old patient with SYNGAP1 gene defect points to importance of variants in broader splice regions and reveals developmental trajectory of SYNGAP1 associated phenotype: case report

2017
BMC Med Genet
PMCID: 5457574
PMID: 28576131
DOI: 10.1186/s12881-017-0425-4
call_split See protocol

[…] rediction of the impact of the variant on splicing was performed using programs Human Splicing Finder, MaxEnt, NNSPLICE, NetGene2, ESEfinder, Alternative Splice Site Predictor (ASSP), Splice Port and Cryp-Skip (see Additional file for details on primer sequences and data analysis). RNA was extracted from whole blood of the patient, her parents and normal controls using the PAXgene Blood RNA Kit ( […]

library_books

Genetic Testing Confirmed the Early Diagnosis of X Linked Hypophosphatemic Rickets in a 7 Month Old Infant

2015
PMCID: 4748509
PMID: 26904698
DOI: 10.1177/2324709615598167

[…] k (http://www.fruitfly.org/seq_tools/splice.html) to predict putative 5′ splice donor and 3′ splice acceptor sites. Potential exon-skipping and activation of cryptic splice sites were predicted using CRYP-SKIP (http://cryp-skip.img.cas.cz/). Both wild-type and mutant flanking intronic sequences of exon 10 of the PHEX gene were subjected to analysis using default parameters. […]

call_split

A Splice Mutation and mRNA Decay of EXT2 Provoke Hereditary Multiple Exostoses

2014
PLoS One
PMCID: 3984245
PMID: 24728384
DOI: 10.1371/journal.pone.0094848
call_split See protocol

[…] g aberrations was done using two different web-based programs designed to detect putative splice sites, taking into account branch points, exonic and intronic motifs, and several regulatory proteins. CRYP-SKIP (http://cryp-skip.img.cas.cz/) was used to estimate the probability of cryptic splice-site activation (PCR-E) and exon skipping (1-PCR-E) as a result of splicing mutations . The CRYP-SKIP al […]

library_books

In silico tools for splicing defect prediction A survey from the viewpoint of end users

2013
PMCID: 4029872
PMID: 24263461
DOI: 10.1038/gim.2013.176

[…] (ASSA, http://splice.uwo.ca/, free registration required): information theory-based models by which changes in the affinity of potential splice and regulatory sites caused by mutation are calculated; CRYP-SKIP (http://cryp-skip.img.cas.cz/): multiple logistic regression model which distinguishes exons that are skipped and that activate cryptic splice sites as a result of splicing mutations; and Sp […]


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CRYP-SKIP institution(s)
University of Southampton School of Medicine, Division of Human Genetics Mailpoint, Southampton, UK

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