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MOTIVATION RNA-Seq technology is promising to uncover many novel alternative splicing events, gene fusions and other variations in RNA transcripts. For an accurate detection and quantification of transcripts, it is important to resolve the mapping ambiguity for those RNA-Seq reads that can be mapped to multiple loci: >17% of the reads from mouse RNA-Seq(More)
A major challenge for next generation sequencing technology is genome assembly. A physical map could be used as a preliminary step towards genome sequencing in a hybrid approach. In this paper, we illustrate a robust physical mapping algorithm, GAPM, which could well complement with the assembly of short fragments. The physical mapping problem (PMP) is to(More)
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