Skip to main content

Table 1 Evaluation of localized alignments. 10395 mouse mRNAs and 2007 zebrafish mRNAs are aligned to the orthologous regions in the human genome.

From: A cross-species alignment tool (CAT)

Mouse mRNA to Human genome
  CDS+UTR (nucl. level) CDS alone (nucl. level) CDS alone (exon level) Speed (mRNA/hr)
Algorithm Sn Sp Sn Sp Sn Sp  
CAT 0.765 0.961 0.924 0.968 0.855 0.893 3579
est2genome 0.772 0.963 0.926 0.970 0.856 0.895 17
GeneWise n/a n/a 0.927 0.972 0.869 0.917 8
Exonerate 0.385 0.983 0.589 0.977 0.495 0.791 1254
exonerate-aa n/a n/a 0.856 0.977 0.787 0.890 10027
BLAT 0.487 0.976 0.678 0.973 0.161 0.172 5138
BLAT-dnax 0.615 0.979 0.872 0.975 0.513 0.518 1172
sim4 0.535 0.977 0.743 0.976 0.524 0.569 36815
Zebrafish mRNA to Human genome
  CDS+UTR (nucl. level) CDS alone (nucl. level) CDS alone (exon level) Speed (mRNA/hr)
Algorithm Sn Sp Sn Sp Sn Sp  
CAT 0.489 0.963 0.803 0.957 0.645 0.754 2806
est2genome 0.463 0.968 0.764 0.961 0.590 0.750 41
GeneWise n/a n/a 0.862 0.975 0.781 0.879 12
exonerate-aa n/a n/a 0.652 0.975 0.543 0.772 6757
  1. The ''correct'' answers, against which we judge these algorithms, are based on an alignment of human mRNAs from RefSeq to the sequence of the human genome, as annotated in the UCSC browser.