Fig. 2

Assembly of At1g01230 using the SRAssembler strategy. The cDNA sequence of At1g01230.1 (blue) and the protein sequence of Os07g26940.1 (black) are shown aligned to the final contig (red) produced by SRAssembler after 4 rounds of assembly using reads data simulating 20X coverage of Arabidopsis chromosome 1. The reads found in each round of the SRAssembler run of At1g01230 are also mapped onto the final contig. Mapped reads are shown as pink or blue rectangles, representing forward and reverse orientation relative to the contig. In the initial round, reads were identified that align with each exon of the query protein. Because we simulated paired-end reads, some of the mapped reads align to the introns of the target gene. The mapped reads become the query contigs for subsequent searches of the read library, “walking” further into the introns and out along the chromosome