Browsing articles tagged with " mRNA splicing"

March 17, 2015. Review article on mRNA splicing mutations highlighted on F1000Research blog

Mar 18, 2015   //   by Peter Rogan   //   product, Software  //  Comments Off

Revised version of our review article on mRNA splicing in F1000Research has been highlighted in the Faculty of 1000 blog:

The blog entry includes links to our YouTube video:

Short version (3:42)

Long version (9:41)


Feb 14, 2013   //   by Peter Rogan   //    //  Comments Off

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Automated Splice Site and Exon Definition Analysis Server (ASSEDA)

ASSEDA has been incorporated into Cytognomix’s MutationForecaster system. ASSEDA is described in Prediction of Mutant mRNA Splice Isoforms by Information Theory-Based Exon Definition by  Mucaki et al. 2013.

Shannon pipeline for mRNA splicing and transcription factor binding site  mutation analysis (SP)

SP has been incorporated into Cytognomix’s MutationForecaster system.    SP for splicing mutations is described in Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences (Shirley et al. 2013), for transcription factor binding sites in Mucaki et al. 2016, Caminsky et al. 2016, and Lu et al. 2016.

Veridical, for verification of predicted mRNA splicing mutations

Veridical sets the standard for evidence-based, statistical validation of mutation predictions from the Shannon pipeline – or other sources.  Veridical has been incorporated into the MutationForecaster system. Veridical is described in Validation of predicted mRNA splicing mutations using high-throughput transcriptome data by Viner et al. 2014.

Variant effect predictor (VEP)

Predict of the effect of variants on coding regions of genes and protein sequence. SIFT and PolyPhen scores are also generated.

Cytognomix user variation database (CUVD)

Store results generated by any of our web tools at the click of a button for variants present in your sample. Variants can be directly related to public data in HGNC, NCBI, EBI, ClinVar, as well as locus specific databases. Based upon the Leiden Open Variation Database.

Cytogenetic Visual Analytic Decision Support Tool (CVDST)

Link literature evidence for gene mutations detected with VEP and SP with this tool. View your results from these other tools with our built-in genome browser. This tool also provides tracks for Cytognomix FISH probes and capture reagents.

After registration with MutationForecaster, subscriptions can be activated through the Account menu on the system.

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January 4, 2013. Paper: “Predicting mRNA transcript isoforms derived from splicing mutations”, ASSEDA server

Jan 5, 2013   //   by Peter Rogan   //   Software  //  Comments Off

Volume 34, Issue 4

“Prediction of mutant mRNA splice isoforms by information theory-based exon definition,” by Eliseos Mucaki, Ben Shirley and Peter Rogan has been accepted for publication by the journal Human Mutation.

Abstract.  Mutations that affect mRNA splicing often produce multiple mRNA isoforms, resulting in complex molecular phenotypes. Definition of an exon and its inclusion in mature mRNA relies on joint recognition of both acceptor and donor splice sites. This study predicts cryptic and exon skipping isoforms in mRNA produced by splicing mutations from the combined information contents (Ri, which measures binding site affinity) and distribution of the splice sites defining these exons. The total information content of an exon (Ri,total) is the sum of the Ri values of its acceptor and donor splice sites, adjusted for the distance separating these sites, ie. the gap surprisal. Differences between total exon information contents (ΔRi,total) are predictive of the relative abundance of these exons in distinct processed mRNAs. Constraints on splice site and exon selection are used to eliminate non-conforming and poorly expressed isoforms. Molecular phenotypes are computed by the Automated Splice Site and Exon Definition Analysis server (ASSEDA; Predictions of splicing mutations were highly concordant (85.2%; n=61) with published expression data. In silico exon definition analysis will contribute to streamlining assessment of abnormal and normal splice isoforms resulting from mutations.

Update: The paper is now available online from the Journal website: DOI: 10.1002/humu.22277 and is cited on PubMed.

Update 2: John Mucaki has produced a Video Tutorial on using the ASSEDA server on YouTube.

Update 3:  The accepted paper has now been copyedited,  typeset and published online: Supplementary data are available as well.  (2-21-2013)

Update 4:  Annual subscriptions to the Automated Splice Site and Exon Definition server are available through Cytognomix  (2-22-2013).

Update 5: The paper has been highlighted in the April 2013 issue of the Journal, where it appeared.  Bing Yu, University of Sydney, authored the commentary (Vol 34[4], page v).

Update 6:  Mucaki EJ., Shirley BC, and Rogan PK. Prediction of Mutant mRNA Splice Isoforms by Information Theory-Based Exon Definition has been published in print. Human Mutation, April 2013, Volume 34 (4), pages 557–565. The journal has made the paper FREE for anyone to download.


Oct 20, 2012   //   by Peter Rogan   //    //  Comments Off


Review article on information theory-based splicing mutation analysis:

Caminsky et al. 2014, Videos describing this paper: short and long versions.