ASSEDA statistics

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Citations per year

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

This map represents all the scientific publications referring to ASSEDA per scientific context
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Associated diseases

This word cloud represents ASSEDA usage per disease context
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Protocols

ASSEDA specifications

Information


Unique identifier OMICS_02629
Name ASSEDA
Alternative name Automatic Splice Site and Exon Definition Analysis
Interface Web user interface
Restrictions to use License purchase required
Programming languages Perl
License Commercial
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Peter Rogan

Publication for Automatic Splice Site and Exon Definition Analysis

ASSEDA citations

 (6)
call_split

Functional assessment of the BMPR2 gene in lymphoblastoid cell lines from Graves’ disease patients

2017
J Cell Mol Med
PMCID: 5824380
PMID: 29266775
DOI: 10.1111/jcmm.13425
call_split See protocol

[…] hnical University of Denmark, Kongens Lyngby, Denmark), Splice View, Human Splicing Finder 2.4.1 version (Aix Marseille Université, Marseille, France) and Automated Splice Site Exon Definition Server‐ASSEDA (University of Western Ontario, London, Canada). […]

call_split

Whole exome sequencing as a diagnostic tool for patients with ciliopathy like phenotypes

2017
PLoS One
PMCID: 5553726
PMID: 28800606
DOI: 10.1371/journal.pone.0183081
call_split See protocol

[…] encoded proteins and other ciliary proteins. When appropriate, the potential effect on splice sites was assessed using several prediction tools: NNSplice [], NetGene2 [], Human Splicing Finder [] and ASSEDA [], all with default settings. Finally, WES data were used to check if candidate variants localize in runs of homozygosity (ROH) regions, what is expected in consanguineous cases. Thus, homozyg […]

call_split

Functional analysis by minigene assay of putative splicing variants found in Bardet–Biedl syndrome patients

2017
J Cell Mol Med
PMCID: 5618670
PMID: 28502102
DOI: 10.1111/jcmm.13147
call_split See protocol

[…] rkeley Drosophila Genome Project (http://www.fruitfly.org/seq_tools/splice.html) , Human Splicing Finder (HSF) 2.4.1 version (http://www.umd.be/HSF/) and Automated Splice Site Exon Definition Server‐ASSEDA (http://splice.uwo.ca/) . Finally, ESE sequences were predicted with Relative Enhancer and Silencer Classification by Unanimous Enrichment‐Rescue ESE (http://genes.mit.edu/burgelab/rescue-ese/) […]

call_split

In Vivo Analysis of Disease Associated Point Mutations Unveils Profound Differences in mRNA Splicing of Peripherin 2 in Rod and Cone Photoreceptors

2016
PLoS Genet
PMCID: 4722987
PMID: 26796962
DOI: 10.1371/journal.pgen.1005811
call_split See protocol

[…] To predict the splicing of the single PRPH2 point mutants, a free trial ASSEDA splice software (splice.uwo.ca/) and open access NNSplice (Berkeley Drosophila Genome Project, http://www.fruitfly.org/seq_tools/splice.html) software were used. […]

library_books

RNA Binding Proteins: Splicing Factors and Disease

2015
Biomolecules
PMCID: 4496701
PMID: 25985083
DOI: 10.3390/biom5020893

[…] lice site strength (MaxEntScan) [], predict splice site usage (NetGene2) [], identify splice site motifs (RESCUE-ESE) [], as well as predict the effect of mutations in both canonical splicing motifs (ASSEDA) [] and auxiliary motifs (Spliceman) []. Spliceman for example, uses the positional distribution of hexamer motifs around exon intron junctions to predict variants outside of canonical splice s […]

library_books

Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information theoretical analysis

2014
F1000Res
PMCID: 4329672
PMID: 25717368
DOI: 10.5256/f1000research.6038.r6917

[…] ion with a proximate, correctly oriented, pre-existing cryptic splice site of opposite polarity , . Insufficient numbers of examples of mutations creating cryptic exons have been reported to date for ASSEDA to accurately predict these exons by default.Several results were generated by incorrect entry of mutations in to ASSA/ASSEDA. For example, altered cryptic splice sites have been confused with […]


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ASSEDA institution(s)
Department of Biochemistry, Western University, London, ON, Canada; Department of Computer Science, Western University, London, ON, Canada
ASSEDA funding source(s)
Natural Sciences and Engineering Research Council of Canada (371758-2009); Canadian Breast Cancer Foundation; Canada Foundation For Innovation; Canada Research Chairs; Compute Canada; Western University; Cytognomix Inc.

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