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Description

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-This track contains RefSeq 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 $organism. -

- - - -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 23 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 -relationship is used in the chains and nets to improve the synteny prediction. -

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Display Conventions and Configuration

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-This track follows the display conventions for -PSL alignment tracks.

-This track may also be configured to display codon coloring, a feature that -allows the user to quickly compare cDNAs against the genomic sequence. For more -information about this option, click -here. -Several types of alignment gap may also be colored; -for more information, click -here. - -

Methods

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Source transcript alignments were obtained from vertebrate organisms - in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank - mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, - were used as available. -
For all vertebrate assemblies that had BLASTZ alignment chains and - nets to the $organism ($db) genome, a subset of the alignment chains were - selected as follows: -
- For organisms whose branch distance was no more than 0.5 - (as computed by phyloFit, see Conservation track description for details), - syntenic filtering was used. Reciprocal best nets were used if available; - otherwise, nets were selected with the netfilter -syn command. - The chains corresponding to the selected nets were used for mapping. -
- For more distant species, where the determination of synteny is difficult, - the full set of chains was used for mapping. This allows for more genes to - map at the expense of some mapping to paralogus regions. The - post-alignment filtering step removes some of the duplications. -
-
The pslMap program was used to do a base-level projection of - the source transcript alignments via the selected chains - to the $organism genome, resulting in pairwise alignments of the source transcripts to - the genome. -
The resulting alignments were filtered with pslCDnaFilter - with a global near-best criteria of 0.5% in finished genomes - (human and mouse) and 1.0% in other genomes. Alignments - where less than 20% of the transcript mapped were discarded. -

- -

-To ensure unique identifiers for each alignment, cDNA and gene accessions were -made unique by appending a suffix for each location in the source genome and -again for each mapped location in the destination genome. The format is: -

-   accession.version-srcUniq.destUniq
-

- -Where srcUniq is a number added to make each source alignment unique, and -destUniq is added to give the subsequent TransMap alignments unique -identifiers. -

-For example, in the cow genome, there are two alignments of mRNA BC149621.1. -These are assigned the identifiers BC149621.1-1 and BC149621.1-2. -When these are mapped to the human genome, BC149621.1-1 maps to a single -location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 -maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note -that multiple TransMap mappings are usually the result of tandem duplications, where both -chains are identified as syntenic. -

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Credits

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-This track was produced by Mark Diekhans at UCSC from cDNA sequence data -submitted to the international public sequence databases by -scientists worldwide.

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References

-Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, -Lau C et al. - -Targeted discovery of novel human exons by comparative genomics. -Genome Res. 2007 Dec;17(12):1763-73. -PMID: 17989246; PMC: PMC2099585 -

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-Stanke M, Diekhans M, Baertsch R, Haussler D. - -Using native and syntenically mapped cDNA alignments to improve de novo gene finding. -Bioinformatics. 2008 Mar 1;24(5):637-44. -PMID: 18218656 -

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-Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. - -Comparative genomics search for losses of long-established genes on the human lineage. -PLoS Comput Biol. 2007 Dec;3(12):e247. -PMID: 18085818; PMC: PMC2134963 -