This article is part of the supplement: Selected articles from the Ninth Asia Pacific Bioinformatics Conference (APBC 2011)

Open Access Research

UMARS: Un-MAppable Reads Solution

Sung-Chou Li123, Wen-Ching Chan124, Chun-Hung Lai3, Kuo-Wang Tsai3, Chun-Nan Hsu45, Yuh-Shan Jou3, Hua-Chien Chen6, Chun-Hong Chen7 and Wen-chang Lin13*

Author Affiliations

1 Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan

2 Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan

3 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

4 Institute of Information Sciences, Academia Sinica, Taipei, Taiwan

5 Information Sciences Institute, University of Southern California, Marina del Rey, CA 90292, USA

6 Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan

7 Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan

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BMC Bioinformatics 2011, 12(Suppl 1):S9  doi:10.1186/1471-2105-12-S1-S9

Published: 15 February 2011

Additional files

Additional file 1:

The refFlat version, genome version, number of transcript, number of exon-exon junction and scientific names of the 21 species.

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Additional file 2:

The sequencing platform, RNA source species, RNA source tissue of these libraries.

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Additional file 3:

Primer sequences involved in this study.

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Additional file 4:

The mapped reads and their corresponding genomic loci. In the Region info column, “-” denoted intergenic regions without known gene annotation. SN. denoted serial numbers of each mapping match.

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Additional file 5:

The detected isomiRs of EBV pre-miRNAs.

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Additional file 6:

PCR experimental validation of the detected EEJ, NM_021019 (7:2-4). The description of the marker lane and the abbreviations are the same with the ones of Fig. 4c. The forward and reverse primers were located at exon 2 and exon 4, respectively. (a) The PCR result showed that the expected EEJ (d transcript) can be experimentally detected. Besides, the major c and the minor d transcripts, the c alternative transcript (with 108 bp fewer than c transcript) was also detected. Both of the detected c alternative and d transcript have EST evidences. (b) The sequencing result provided the authenticity of the detected EEJs.

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Additional file 7:

PCR experimental validation of the detected EEJ, NM_178580 (13:10-13). The description of the marker lane and the abbreviations are the same with the ones of Fig. 4c. The forward and reverse primers were located at exon 10 and exon 13, respectively. (a) The PCR result showed that the expected EEJ (d2 transcript) can be experimentally detected. A c alternative transcript (with 56 bp more than c transcript) was also detected. In addition the d2 transcript (with exon 11 and 12 skiping), we also detected a d1 transcript (with exon 12 skipping, not originally detected by UMARS). (b) The sequencing result provided the authenticity of the detected EEJs.

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Additional file 8:

The information of all detected discrete EEJs. Values in this table are tab separated and can be opened with Excel.

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