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2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2015)
Washington, DC, USA
Nov. 9, 2015 to Nov. 12, 2015
ISBN: 978-1-4673-6798-1
pp: 1536-1542
Xiaodong Cui , Department of Electrical and Computer Engineering, University of Texas at San, San Antonio, 78230, USA
Zhen Wei , Department of Biological Sciences, XJTLU-Huai'an Research Institute of New-type Urbanization, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
Lin Zhang , School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, 221116, China
Hui Liu , School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, 221116, China
Lei Sun , School of Information Engineering, Yangzhou University, Jiangsu 225127, China
Shao-Wu Zhang , Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, Shaanxi, 710027, China
Yufei Huang , Department of Electrical and Computer Engineering, University of Texas at San, San Antonio, 78230, USA
Jia Meng , Department of Biological Sciences, XJTLU-Huai'an Research Institute of New-type Urbanization, Xi'an Jiaotong-Liverpool, University, Suzhou, Jiangsu 215123, China
ABSTRACT
Biological features, such as, genes, transcription factor binding sites, SNPs, etc., are usually denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective, it can be tedious to examine the distribution of RNA-related genomic features on RNA transcripts with existing tools due to the conversion and comparison between genome-based coordinates to RNA-based coordinates. We developed here an open source R package Travis for sketching the transcriptomic view of genomic features so as to facilitate the analysis of RNA-related but genome-based coordinates. Internally, Travis package extracts the coordinates relative to the landmarks of transcripts, with which the distribution of RNA-related genomic features can then be conveniently analyzed. We demonstrated the usage of Travis package in analyzing post-transcriptional RNA modifications (5-MethylCytosine and N6-MethylAdenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq). The Travis R package is now publicly available from GitHub: https://github.com/lzcyzm/Travis.
INDEX TERMS
Genomic Features, visualization, RNA, N6-MethylAdenosine (m6A), 5-MethylCytosine (m5C), BS-Seq, MeRIP-Seq, R package
CITATION

X. Cui et al., "Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates," 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington, DC, USA, 2015, pp. 1536-1542.
doi:10.1109/BIBM.2015.7359904
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