Title :
An SVM-based approach for discovering splicing junctions with RNA-Seq
Author :
Chong Chu ; Yufeng Wu
Author_Institution :
Comput. Sci. & Eng., Univ. of Connecticut, Storrs, CT, USA
Abstract :
Because of the complicity of RNA splicing, discovering splicing junctions and aligning RNA-Seq reads with high sensitivity and specificity is still a challenging problem. In this paper, we propose an SVM-based approach for discovering splicing junctions with RNA-Seq data. The key idea of our approach is combining multiple sources of information contained in sequence data in discovering exon-intron boundaries. Results on simulated data suggest that our approach works well.
Keywords :
RNA; biology computing; molecular biophysics; molecular configurations; support vector machines; RNA-seq data; SVM-based approach; exon-intron boundaries; multiple sources; sequence data; splicing junctions; Algorithm design and analysis; Bioinformatics; Genomics; Junctions; RNA; Sensitivity; Splicing; RNA-Seq reads alignment; Splicing junctions discovery; support vector machine;
Conference_Titel :
Computational Advances in Bio and Medical Sciences (ICCABS), 2014 IEEE 4th International Conference on
Conference_Location :
Miami, FL
Print_ISBN :
978-1-4799-5786-6
DOI :
10.1109/ICCABS.2014.6863943
