Sensitivity of WU-TBLASTX andBLAT Applied to 13 Million Mouse Shotgun Reads and Human Chromosome 22
| Method | % Chr 22 | % RefSeq bases | Enrichment | % RefSeq exons |
| WU-TBLASTX | 2.67% | 81.7% | 31x | 84.5% |
| BLAT | 2.89% | 80.8% | 28x | 86.7% |
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The “% Chr22” column shows the percentage of chromosome 22 covered by the alignments (genomic density). The next column is the percentage of bases inside of human RefSeq coding sequences covered by the alignments (RefSeq coding density). “Enrichment” is the ratio of the RefSeq coding density compared to genomic density. Higher levels of enrichment indicate more specificity at the base level. The last column shows the percentage of RefSeq coding exons where any part of the exon is covered by an alignment. WU-TBLASTX was run with the parameters described in the second row of Table 1.BLAT was run with using a pair-of-4-mers seed and a score cut off of 30. At these settings, BLAT touches slightly more exons, but WU-TBLASTX covers slightly more bases in exons.
