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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 human. 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.
To view the full description, click here.
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