18327e879f9df894313dd3100084c94cc6dd4136 hiram Fri Dec 5 11:03:40 2025 -0800 track definitions for TOGA version 2 refs #35776 diff --git src/hg/makeDb/trackDb/TOGAv2.html src/hg/makeDb/trackDb/TOGAv2.html new file mode 100644 index 00000000000..88e73527fc1 --- /dev/null +++ src/hg/makeDb/trackDb/TOGAv2.html @@ -0,0 +1,85 @@ +

Description

+TOGA version 2.0 +(Tool to infer Orthologs from Genome Alignments) +is a homology-based method that integrates gene annotation, inferring +orthologs and classifying genes as intact or lost. +

+ +

Methods

+As input, TOGA uses a gene annotation of a reference species +(human/hg38 for mammals, chicken/galGal6 for birds) and +a whole genome alignment between the reference and query genome. +

+TOGA implements a novel paradigm that relies on alignments of intronic +and intergenic regions and uses machine learning to accurately distinguish +orthologs from paralogs or processed pseudogenes. +

+To annotate genes, +CESAR 2.0 +is used to determine the positions and boundaries of coding exons of a +reference transcript in the orthologous genomic locus in the query species. +

+ +

Display Conventions and Configuration

+Each annotated transcript is shown in a color-coded classification as +

+ "intact": middle 80% of the CDS + (coding sequence) is present and exhibits no gene-inactivating mutation. + These transcripts likely encode functional proteins.
+ "partially intact": 50% of the CDS + is present in the query and the middle 80% of the CDS exhibits no + inactivating mutation. These transcripts may also encode functional + proteins, but the evidence is weaker as parts of the CDS are missing, + often due to assembly gaps.
+ "missing": <50% of the CDS is present + in the query and the middle 80% of the CDS exhibits no inactivating + mutation.
+ "uncertain loss": there is 1 + inactivating mutation in the middle 80% of the CDS, but evidence is not + strong enough to classify the transcript as lost. These transcripts may + or may not encode a functional protein.
+ "lost": typically several inactivating + mutations are present, thus there is strong evidence that the transcript + is unlikely to encode a functional protein.

+Clicking on a transcript provides additional information about the orthology +classification, inactivating mutations, the protein sequence and protein/exon +alignments. +

+ +

Credits

+This data was prepared by the Michael Hiller Lab +

+ +

References

+The TOGA software is available from +github.com/hillerlab/TOGA +

+ +

+Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos +DG, Hilgers L et al. + +Integrating gene annotation with orthology inference at scale. +Science. 2023 Apr 28;380(6643):eabn3107. +PMID: 37104600; PMC: PMC10193443 +