UMARS: Un-MAppable Reads Solution

BMC Bioinformatics

Research

Chun-Hong Chen¹  Sung-Chou Li²  Wen-Ching Chan³  Wen-chang Lin⁴  Yuh-Shan Jou⁵  Chun-Hung Lai⁵  Kuo-Wang Tsai⁵  Chun-Nan Hsu⁶  Hua-Chien Chen⁷ 

[1] Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan;Institute of Information Sciences, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan;Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan;Institute of Information Sciences, Academia Sinica, Taipei, Taiwan;Information Sciences Institute, University of Southern California, 90292, Marina del Rey, CA, USA;Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan;

关键词: Splice Isoforms;    Viral miRNAs;    Redundancy Problem;    Alternative Splice Isoforms;    Polymerase Chain Reaction Component;   

DOI  :  10.1186/1471-2105-12-S1-S9

来源: Springer

【 摘 要 】

BackgroundUn-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequencing (NGS) technology has emerged as a powerful tool for generating high-throughput sequencing data and has been applied to many kinds of biological research. In a typical analysis, adaptor-trimmed NGS reads were first mapped back to reference sequences, including genomes or transcripts. However, a fraction of NGS reads failed to be mapped back to the reference sequences. Such un-mappable reads are usually imputed to sequencing errors and discarded without further consideration.MethodsWe are investigating possible biological relevance and possible sources of un-mappable reads. Therefore, we developed UMARS to scan for virus genomic fragments or exon-exon junctions of novel alternative splicing isoforms from un-mappable reads. For mapping un-mappable reads, we first collected viral genomes and sequences of exon-exon junctions. Then, we constructed UMARS pipeline as an automatic alignment interface.ResultsBy demonstrating the results of two UMARS alignment cases, we show the applicability of UMARS. We first showed that the expected EBV genomic fragments can be detected by UMARS. Second, we also detected exon-exon junctions from un-mappable reads. Further experimental validation also ensured the authenticity of the UMARS pipeline. The UMARS service is freely available to the academic community and can be accessed via http://musk.ibms.sinica.edu.tw/UMARS/.ConclusionsIn this study, we have shown that some un-mappable reads are not caused by sequencing errors. They can originate from viral infection or transcript splicing. Our UMARS pipeline provides another way to examine and recycle the un-mappable reads that are commonly discarded as garbage.

【 授权许可】

Unknown   
© Li et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.