Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (siamang - 2024-01-05 - National Human Genome Research Institute, National Institutes of Health).

This is a composite track with both a multiz calculated multiple alignment and the same set of assemblies used to calculate the 11-way multiple alignment with the cactus alignment procedure.

The multiz multiple alignment is generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level. The following conventions are used:

• Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the siamang - 2024-01-05 - National Human Genome Research Institute, National Institutes of Health genome or a lineage-specific deletion between the aligned blocks in the aligning species.
• Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
• Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

• Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
• Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the siamang - 2024-01-05 - National Human Genome Research Institute, National Institutes of Health genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the siamang - 2024-01-05 - National Human Genome Research Institute, National Institutes of Health sequence at those alignment positions relative to the longest non-siamang sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

count	alignment percent	assembly and browser link	maf file type	common name/assembly date assembly submitter
01	n/a	GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri	reference	siamang (v2 Jambi primary hap 2024)/2024-01-05
02	81.412	GCA_028885625.2	syntenic net	Bornean orangutan/2024-01-08/NHGRI/NIH
03	81.382	GCA_029281585.2	syntenic net	western lowland gorilla/2024-01-08/NHGRI/NIH
04	81.379	GCA_028885655.2	syntenic net	Sumatran orangutan/2024-01-05/NHGRI/NIH
05	81.295	hg38	syntenic net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
06	81.290	GCA_028858775.2	syntenic net	chimpanzee/2024-01-08/NHGRI/NIH
07	81.285	GCA_029289425.2	syntenic net	pygmy chimpanzee/2024-01-08/NHGRI/NIH
08	81.278	hs1	syntenic net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
09	62.736	GCF_011100555.1	maf net	white-tufted-ear marmoset/2021-04-28/VGP
10	29.935	GCF_020740605.2	maf net	Ring-tailed lemur/2021-11-04/VGP
11	13.927	GCF_027406575.1	maf net	slow loris/2022-12-28/VGP

Alignments identity

showing percent identity, how much of the target is matched by the query

chains	syntenic	reciprocal best	common name	assembly
81.412	80.736	77.837	Bornean orangutan	GCA_028885625.2
81.382	80.559	77.455	western lowland gorilla	GCA_029281585.2
81.379	80.705	77.828	Sumatran orangutan	GCA_028885655.2
81.295	80.447	77.315	Human	hg38
81.290	80.505	77.400	chimpanzee	GCA_028858775.2
81.285	80.442	77.384	pygmy chimpanzee	GCA_029289425.2
81.278	80.475	77.353	Human	hs1
62.736	61.843	60.015	white-tufted-ear marmoset	GCF_011100555.1
29.935	29.277	28.347	Ring-tailed lemur	GCF_020740605.2
13.927	12.972	13.320	slow loris	GCF_027406575.1

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Methods

Pairwise alignments of each species to the siamang//hive/data/genomes/asmHubs/genbankBuild/GCA/028/878/055/GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri/html/GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri.names.tab/GCA_028878055.2/2024-01-05 genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

From the cactus alignment, a target specific maf file was extracted from the cactus hal file. This maf file is used to construct the track.

Credits

This track was created using the following programs:

• Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
• Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
• Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
• MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
• Tree image generator: phyloPng by Galt Barber, UCSC
• Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

References

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

PhyloP:

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. PMID: 15965027; PMC: PMC1172034; DOI: 10.1101/gr.3577405

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. DOI: 10.1007/0-387-27733-1_12

Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. DOI: 10.1007/11732990_17

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. DOI: 10.1038/s41586-020-2871-y; PMID: 33177663; PMC: PMC7673649