-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 LASTZ or BLASTZ alignment chains, resulting -in a prediction of the orthologous genes in $organism. For more distant -organisms, reciprocal best alignments are used. -
- -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. -
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