SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers

RNA splicing is a cellular process driven by the interaction between numerous regulatory sequences and binding sites, however, such interactions have been primarily explored by laboratory methods since computational tools largely ignore the relationship between different splicing elements. Current c...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2014-07, Vol.11 (4), p.648-656
Main Authors: Lo, Christine, Kakaradov, Boyko, Lokshtanov, Daniel, Boucher, Christina
Format: Article
Language:English
Subjects:
Algorithms
Approximation algorithms
Binding sites
Bioinformatics
Biology
Computation
Computational biology
Computational Biology - methods
EPTAS
exon splicing enhansers
Exons - genetics
Gene sequencing
Heuristic
Humans
Joints
Polynomials
PTAS
randomized algorithms
Ribonucleic acids
RNA
RNA splicing
RNA Splicing - genetics
Software
Splicing
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Summary:RNA splicing is a cellular process driven by the interaction between numerous regulatory sequences and binding sites, however, such interactions have been primarily explored by laboratory methods since computational tools largely ignore the relationship between different splicing elements. Current computational methods identify either splice sites or other regulatory sequences, such as enhancers and silencers. We present a novel approach for characterizing co-occurring relationships between splice site motifs and splicing enhancers. Our approach relies on an efficient algorithm for approximately solving Consensus Sequence with Outliers , an NP-complete string clustering problem. In particular, we give an algorithm for this problem that outputs near-optimal solutions in polynomial time. To our knowledge, this is the first formulation and computational attempt for detecting co-occurring sequence elements in RNA sequence data. Further, we demonstrate that SeeSite is capable of showing that certain ESEs are preferentially associated with weaker splice sites, and that there exists a co-occurrence relationship with splice site motifs.
ISSN:1545-5963
1557-9964
DOI:10.1109/TCBB.2014.2304294