These tracks contain cDNA and gene alignments produced by the
TransMap cross-species alignment algorithm from other vertebrate
species in the UCSC Genome Browser. For closer evolutionary
distances, the alignments are created using syntenically
filtered BLASTZ alignment chains, resulting in a prediction of
the orthologous genes in human.TransMap maps genes and related
annotations in one species to another using synteny-filtered
pairwise genome alignments (chains and nets) to determine the
most likely orthologs. For example, for the mRNA TransMap track
on the human assembly, more than 400,000 mRNAs from 25
vertebrate species were aligned at high stringency to the native
assembly using BLAT. The alignments were then mapped to the
human assembly using the chain and net alignments produced using
blastz, which has higher sensitivity than BLAT for diverged
organisms. Compared to translated BLAT, TransMap finds fewer
paralogs and aligns more UTR bases. For closely related low-
coverage assemblies, a reciprocal-best re