Tools predicting problems in mRNA splicing

 

Pre-messenger RNA (pre-mRNA) splicing defects are likely to have an impact on clinical practice as these seem to have a role in almost all known diseases with genetic aetiology  (Tazi et al. 2009). It is likely that approximately 15 % of pathogenic mutations cause disease through the defect that they introduce in the splicing mechanism (Baralle et al 2009). Therefore it is important to have software tools that could predict whether a given variation would interfere with the mRNA splicing.  This site collects together such tools mainly based on review of Baralle et al. 2009.  It must be noted however that these programs are not yet considered to be reliable and any result obtained by in silico  methods should therefore be confirmed by wet lab experiments.  This section also contains tools and articles associated with other RNA  level consequences caused by mutations/SNPs. 

 

 

 

Programs available

An extensive overview of mRNA splicing tools can be found from the recent review  article by Baralle et al.
The program categorisation used here follows the one in the review article.

 

Donor, acceptor and branch-site evaluation programs:

• MaxEntScan (MES)
• Spliceview
• Analyzer Splice Tool (AST)
• Spliceport
• Automated Splice-Site Analyses (ASSA)
  
• HBond
• NetGene2
• Human Splicing Finder (HSF formerly know as SSF)
• Cryp-Skip
• GeneSplicer
• NNSplice

 

Splicing regulatory elements (SREs) evaluation programs:

• ESEfinder
• RESCUE-ESE
• PESX
  
• ExonScan
• ESRsearch
• Splicing Rainbow

 

General Splicing utilities

• Splice Signal Analysis
  
• Sroogle

 

RNA secondary structure evaluation programs

• mFold
• pFold
• SNPfold

 

Tool predicting the effect that SNP could have on transcription:

• PupaSuite

 

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Description of programs

 

Donor, acceptor and branch -site evaluation programs

These methods  tend to be more accurate than programs evaluating SREs. This is due to the fact that the donor and acceptor elements are more conserved than SREs (Baralle et al 2009).

 

MES (MaxEntScan)

MES is unable to read through the sequence and find the splice site. The user has to indicate the exon-intron junktion in the short nucleotide sequence tested. Knowledge of putative splice site is consequently a prerequisite when working with MES. However, the algorithm can be used through Alamut which circumvents this problem.

website: MES

Download:

Reference: Yeo et al. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J.Comput.Biol., 2004, 11, 2-3, 377-394. doi:10.1089/1066527041410418

 

Spliceview

website: Spliceview

Download:

Reference:Rogozin I.B. and L. Milanesi. Analysis of donor splice signals in different organisms. J. Mol. Evol., 1997, V.45, 50-59.

 

Analyzer  Splice Tool (AST)

website: AST

Download:

Reference:

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Spliceport

website: Spliceport

Download:

Reference: Dogan et al. SplicePort: An Interactive Splice-Site Analysis Tool. Nucleic Acids Research, 2007. doi:10.1093/nar/gkm407

 

Automated Splice-Site Analyses (ASSA)

website: ASSA

Download:

Reference:

 

HBond

website: HBond

Download:

Reference:

 

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NetGene2

website: NetGene2

Download: here

Reference:Brunak et al. Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence, Journal of Molecular Biology, 1991, 220, 49-65. doi:10.1016/0022-2836(91)90380-O    

 

HSF (Human Splicing Finder)

website: HSF

Download:

Reference:Desmet et al. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res., 2009, 37, 9, e67  doi:10.1093/nar/gkp215

 

 

Cryp-Skip

website: Cryp-Skip

Download:

Reference:

 

NNSplice

Also available through Alamut.

website: NNSplice

Download:

Reference:Reese MG, Eeckman, FH, Kulp, D, Haussler, D, 1997. ``Improved Splice Site Detection in Genie''. J Comp Biol 4(3), 311-23.

 

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Splicing regulatory elements (SREs) evaluation programs

 

ESEfinder

ESEfinder (Cartegni et al 2003) is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs and to predict whether exonic mutations disrupt such elements. It implements motif-scoring matrices. Possible drawback of this program is that it searches the ESE motifs corresponding only to four SR proteins. This means that sequences corresponding to the RNA binding specificities of other SR proteins or for other types of proteins will be missed by the program.

website: ESEfinder

Download:

Reference: Cartegni et al (2003). ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res., 2003, 31, 13, 3568-3571 . doi: 10.1093/nar/gkg616

 

RESCUE-ESE

RESCUE-ESE predicts motifs with ESE sequences based on the statistical analysis on differences  in hexamer frequencies between exons and introns and between exons with weak and strong splice sites.

website:RESCUE-ESE

Download:

Reference:Fairbrother et al (2004) . RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res., 2004, 32, Web Server issue, W187-90. doi:10.1093/nar/gkh393

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PESX

website:PESX

Download:

Reference:

 

 

ExonScan

website: ExonScan

Download:

Reference:

 

ESRsearch

website: ESRsearch

Download:

Reference:

 

Splicing Rainbow

website: Splicing Rainbow

Download:

Reference:

 

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General splicing utilities

 

Splice Signal Analysis

website: Splice Signal Analysis

Download:

Reference:

 

Sroogle

Sroogle is a webserver for visualization of splicing signals. It provides a graphic display of splicing related data on DNA segments including splice site scores based on different metrics, mapping of putative exonic and intronic splicing regulatory sequences (SRSs), data regarding SRSs that would occur as a result of point mutations and percentile scores comparing your target exon to precompiled datasets of constitutive and alternative exons.

As an input server requests  exons along with the two introns flanking it. The server will accept either consecutive stretches of DNA, or stretches of DNA separated by spaces and numbers, as obtained in the UCSC web browser.

website: Sroogle

Download:

Reference: Schwartz et al.  SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W189-92. Epub 2009 May 8. doi: 10.1093/nar/gkp320

 

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RNA secondary structure evaluation programs

 

mFOLD

website: mFold

Download:mfold version 3.4

Reference:M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-15, (2003) doi:10.1093/nar/gkg595

 

 

pFOLD

pFOLD is RNA secondary structure prediction program using stochastic context-free grammars. It takes an alignment of RNA sequences as input and predicts a common structure for all sequences.

website: pFold

Download:

Reference: Knudsen et al. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 2003, 31, 13, 3423-3428. article

 

SNPfold

For some observed associations the disease phenotype is caused by a structural rearrangement in a regulatory region of the RNA transcript. UTR and SNP combinations identified by the method described in the article are postulated to  constitute a “RiboSNitch,” that is a regulatory RNA in which a specific SNP has a structural consequence that results in a disease phenotype. SNPfold algorithm can help identify RiboSNitches by leveraging GWAS data and an analysis of the mRNA structural ensemble. 

website: SNPfold

Reference: Halvorsen M, Martin JS, Broadaway S, Laederach A, 2010 Disease-Associated Mutations That Alter the RNA Structural Ensemble. PLoS Genet 6(8): e1001074. doi:10.1371/journal.pgen.1001074

 

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Tool predicting the effect that SNP could have on transcription

 

PupaSuite

PupaSuite finds all the SNPs mapping in locations that might cause a loss of functionality in the genes.

website: PupaSuite

Download:

Reference: Conde et al. PupaSuite: finding functional SNPs for large-scale genotyping purposes. Nucl Acids Research, 2006, 34: W621-W625. doi:10.1093/nar/gkl071

 

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Useful databases

Databases were extensively listed in the review article by Baralle et al (2009). The catagorisation of databases follows the one used in the article. A few additional databases have been added in addition to those mentioned in the review article.

 

Splicing  mutations database

• Human Gene Mutation Database (HGMD)
   
• DBASS3 and DBASS5
   
• Alternative Splicing Mutation Database (ASMD)
• list of specialiced databases
  
• 
  
  

 

Alternative splicing database

• ASTD (Alternative Splicing and Transcript Diversity,  successor of ASD and ATD)
  
• Alternative Splicing Prediction Database (ASPicDB)
• ASAPII
• Alternative Splicing database
• MAASE (The Manually Annotated AlternativelySpliced Events)
• ASDB (database of alternatively spliced genes)
•  ASG (Alternative Splicing Gallery)
•  ProSplicer

 

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Review articles

• Baralle et al (2009).  Missed threads. The impact of pre-mRNA splicing defects on clinical practice. EMBO reports 10, 8, 810–816 (2009).  doi:10.1038/embor.2009.170

• Baralle et al. Splicing in action: assessing disease causing sequence changes. J.Med.Genet., 2005, 42, 10, 737-748. doi:10.1136/jmg.2004.029538
• Hartmann et al. (2008) Diagnosis of pathogenic splicing mutations: does bioinformatics cover all the bases? Front Biosci., 13:3252-3272. doi:10.2741/2924
• Hellen, E. (2010) Splice Site analysis tools. NGRL report. pdf

 

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Other articles

• Houdayer,C et al.  Evaluation of in silico splice tools for decision-making in molecular diagnosis.Hum.Mutat., 2008, 29, 7, 975-982. doi:10.1002/humu.20765

 

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Useful Links

• LSAT (text minig tool that collects PubMed entries pertaining alternative splicing)

 

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