Recall and precision for each localization algorithm. Results for SSAHA are shown in red, MegaBLAST in blue, and BLAT in green. The first column represents the recall obtained with full-length gene query sequences. The second column shows the recall obtained with sequence tag queries. The third and fourth columns display the precision of each algorithm when used to localize full-length genes and sequence tags, respectively. (A) Recall and precision at the level of the gene, as measured by overlap of at least one nucleotide between a set of localizations by an algorithm and the region of the genome containing the gene. Cyan lines indicate the recall and precision achieved when only the top hit is considered. (B) Exon recall and precision, as measured by an overlap of at least one nucleotide between the known localization of an exon and a match. Sequence tags are shorter than full-length genes and therefore typically contain sufficient sequence information to match only a few exons of any gene, leading to low recall at the exon and nucleotide levels. This does not indicate failure by the localization programs. (C) Nucleotide recall and precision, as measured by a match between a nucleotide in the known localization of a gene and a nucleotide from a query sequence localization.