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Table 3 Benchmark test on single-cell genome mapping1.

From: JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

Application Running time (s) No of mapped reads2
RMAP 0.7 3 (0.65%)
Maq 3.3 0
JANE 7.1 103 (22.3%)
Exonerate 3980 n.a. 3
  1. 1Example: pori bacteria sequence reads are mapped to the template genome Rhodopirellula Baltica SH1. These are typical long reads (300 bp and more). 2Accuracy of mapping (fingerprint test) was determined as given in materials and methods. 3Exonerate assumes a eukaryotic genome with splicing. Splicing events are introduced by Exonerate if the sequence stretch is short and then an intron (several thousand base pairs) is assumed until the next local match. Thus, in the tough case above, all ESTs mapped (462 from 462) were sliced by Exonerate in several pieces and only short regions were aligned. If there were longer stretches they were mapped to the same region as JANE, but did have shorter length in the alignment.