「A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping」
A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping
［IPSJ Transactions on Bioinformatics Vol.5 pp.27-33］
Whole transcriptome sequencing, often referred to as RNA-Seq, is becoming widely used and is revolutionizing the cataloging isoforms using a vast number of short mRNA fragments called reads. Conventional RNA-Seq analysis methods typically align reads onto a reference genome (mapping) in order to capture the form of isoforms that each gene yields. We propose a method for isoform prediction by iterative mapping. The positions from which reads originate can be estimated based on the information of expression levels, whereas quantification of isoform-level expression requires accurate mapping. These procedures are mutually dependent, and therefore remapping reads is essential. Our method achieved a precision of 66.7% and outperformed conventional methods in terms of the isoform detection rate.
Tomoshige Ohno 君
He received his B.E., M.S., and Ph.D. degrees from Osaka University in 2009, 2011 and 2014, respectively. He currently serves as a bioinformatician at the Pharmaceutical Research Division of Shionogi & Co., Ltd. His research interests include computational biology and sequence analysis.
Shigeto Seno 君
He is an assistant professor of the Graduate School of Information Science and Technology, Osaka University. He received his B.E., M.E., and Ph.D. degrees from Osaka University in 2001, 2003 and 2006, respectively. His research interests include bioinformatics. He is a member of IPSJ, JSBi and MBSJ.
Yoichi Takenaka 君
He is an associate professor of the Graduate School of Information Science and Technology, Osaka University from 2002. He received Research Fellowship for Young Scientists from Japan Society for the Promotion of Science in 1998. He received his Ph.D. (Engineering) from Osaka University in 2000. He was a research associate of the Graduate School of Engineering Science, Osaka University from 2000 to 2002.
Hideo Matsuda 君
He is a professor of the Graduate School of Information Science and Technology, Osaka University from 2002. He received his B.S., M.E., and Ph.D. degrees from Kobe University in 1982, 1984, and 1987, respectively. His research interests include sequence analysis and genetic network reconstruction from genomic data. He is a member of IPSJ, JSBi, ISCB, IEEE CS, and ACM.