한빛사 논문
Jae Y. Hwang1,†, Sungbo Jung1,†, Tae L. Kook1, Eric C. Rouchka1,2, Jinwoong Bok 3,4,5,* and Juw W. Park 1,2,*
1Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA.
2KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA.
3Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
4Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea and 5BK21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
†The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
*Corresponding author
Abstract
The rMAPS2 (RNA Map Analysis and Plotting Server 2) web server, freely available at http://rmaps.cecsresearch.org/, has provided the high-throughput sequencing data research community with curated tools for the identification of RNA binding protein sites. rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. The initial release of rMAPS focused only on the most common alternative splicing event, skipped exon or exon skipping. However, there was a high demand for the analysis of other major types of alternative splicing events, especially for retained intron events since this is the most common type of alternative splicing in plants, such as Arabidopsis thaliana. Here, we expanded the implementation of rMAPS2 to facilitate analyses for all five major types of alternative splicing events: skipped exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site and retained intron. In addition, by employing multi-threading, rMAPS2 has vastly improved the user experience with significant reductions in running time, ∼3.5 min for the analysis of all five major alternative splicing types at once.
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