Comparison of the sensitivity and running time of FANSe and Bowtie on mapping long reads (>140 nt). Escherichia coli genomic DNA sequenced with a 454 GS FLX pyrosequencing platform ( 40 ) was used as a dataset. FANSe was set to allow 3 or 10 mismatches; three mismatches were allowed for Bowtie. Mapping was performed with the indel detection switched on (gray bars) or off (black bars). MM, mismatches.