- Synteny (log10 value): 398
- Global CDS fraction: 0.02385595521683938
- Local CDS fraction: 0.12816666666666668
- Local intron fraction: 0.8041506533435818
- Local CDS coverage: 0.9961139896373057
- Flank fraction: 0.734
For each projection (one reference transcript and one overlapping chain),
TOGA computes the following features by intersecting the reference coordinates of aligning
blocks in the chain with different gene parts (coding exons, UTR (untranslated region) exons, introns)
and the respective intergenic regions.
We define the following variables:
- c: number of reference bases in the intersection between chain blocks and coding exons of the gene under consideration.
- C: number of reference bases in the intersection between chain blocks and coding exons of all genes.
- a: number of reference bases in the intersection between chain blocks and coding exons and introns of the gene under consideration.
- A: number of reference bases in the intersection between chain blocks and coding exons and introns of all genes and the intersection
between chain blocks and intergenic regions (excludes UTRs).
- f: number of reference bases in chain blocks overlapping the 10 kb flanks of the gene under consideration.
Alignment blocks overlapping exons of another gene that is located in these 10 kb flanks are ignored.
- i: number of reference bases in the intersection between chain blocks and introns of the gene under consideration.
- CDS (coding sequence): length of the coding region of the gene under consideration.
- I: sum of all intron lengths of the gene under consideration.
Using these variables, TOGA computes the following features:
- “global CDS fraction” as C / A. Chains with a high value have alignments that largely overlap coding exons,which is a hallmark of paralogous or processed pseudogene chains. In contrast, chains with a low value also align many intronic and intergenic regions, which is a hallmark of orthologous chains.
- “local CDS fraction” as c / a. Orthologous chains tend to have a lower value, as intronic regions partially align. This feature is not computed for single-exon genes.
- “local intron fraction” as i / I. Orthologous chains tend to have a higher value.This feature is not computed for single-exon genes.
- “flank fraction” as f / 20,000. Orthologous chains tend to have higher values,as flanking intergenic regions partially align. This feature is important to detect orthologous loci of single-exon genes.
- “synteny” as log10 of the number of genes, whose coding exons overlap by at least one base aligningblocks of this chain. Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values.
- “local CDS coverage” as c / CDS, which is only used for single-exon genes.
(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.
This track has 43,972 items in the track, covering 443,389,332 bases
in the sequence which is % 42.63 of the total sequence of size
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,
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
"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
The data for this track is available from the bigBed file format
with the command line access tool bigBedToBed available from
the utilities download directory
To extract from the bigBed file:
bigBedToBed "https://hgdownload.soe.ucsc.edu/hubs/GCF/014/805/655/GCF_014805655.1/bbi/HLTOGAannotVsGalGal6v1.bb" togaData.bed
with the result in the togaData.bed
This data was prepared by the Michael Hiller Lab
The TOGA software is available from
Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales A,
Ahmed AW, Kontopoulos DG, Hilgers L, Zoonomia Consortium, Hiller M.
TOGA integrates gene annotation with orthology inference
at scale. bioRxiv preprint September 2022