17ebf3b49d9a9f89f29c9580be6d98f705190cd2 lrnassar Wed Jul 10 09:00:55 2019 -0700 Small changes from CR #23802 diff --git src/hg/makeDb/trackDb/transMapV5.html src/hg/makeDb/trackDb/transMapV5.html index f159c5e..3fa6f12 100644 --- src/hg/makeDb/trackDb/transMapV5.html +++ src/hg/makeDb/trackDb/transMapV5.html @@ -4,22 +4,22 @@ 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 +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.