Figure 1From: Optimal spliced alignments of short sequence readsProposed pipeline: Short reads are first aligned with vmatch to identify unspliced reads. Un-mapped or potentially spliced reads are aligned again to identify reads of at least half of the read length to find seeds for QPALMA. For each seed position QPALMA aligns the read and returns a score. The best scoring alignment is returned as the spliced alignment of the read.Back to article page