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|Title:||TAMeBS: A sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis||Authors:||Sun, Ruimin
|Keywords:||Biological Sciences||Issue Date:||2014||Source:||Sun, R., Tian, Y., & Chen, X. (2014). TAMeBS: A sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis. 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).||Abstract:||Cytosine methylation plays an important role in many biological regulation processes. The current gold-standard method for analyzing cytosine methylation is based on sodium bisulfite treatment and high-throughput sequencing technologies. In this paper we introduce a new tool called TAMeBS for cytosine methylation analysis using bisulfite sequencing data. It aims to align long bisulfite-treated DNA reads onto a reference genome sequence with high mapping efficiency and estimate the methylation status of each cytosine very accurately. Our approach builds on recent advances in alignment techniques, including bidirectional FM-index, approximate seeds, and the likelihood-ratio scoring matrix which was designed particularly for aligning bisulfite-treated DNA reads. We compared TAMeBS with several popular bisulfite-treated read mapping tools on both simulation and real data. Experimental results showed that TAMeBS could detect many more uniquely best mapped reads than other tested tools while achieving a good balance between sensitivity and precision. The source code of TAMeBS is freely available at https://sourceforge.net/projects/tamebs/.||URI:||https://hdl.handle.net/10356/81227
|DOI:||10.1109/BIBM.2014.6999148||Rights:||© 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The published version is available at: [http://dx.doi.org/10.1109/BIBM.2014.6999148].||Fulltext Permission:||open||Fulltext Availability:||With Fulltext|
|Appears in Collections:||SBS Conference Papers|
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