Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (western lowland gorilla - 2024-01-08 - National Human Genome Research Institute, National Institutes of Health).

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

count	alignment percent	assembly and browser link	maf file type	common name/assembly date assembly submitter
01	81.301	hg38	syntenic net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
02	81.201	hs1	syntenic net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
03	79.907	GCA_029289425.2	syntenic net	pygmy chimpanzee/2024-01-08/NHGRI/NIH
04	79.878	GCA_028858775.2	syntenic net	chimpanzee/2024-01-08/NHGRI/NIH
05	79.307	GCA_028885655.2	syntenic net	Sumatran orangutan/2024-01-05/NHGRI/NIH
06	79.288	GCA_028885625.2	syntenic net	Bornean orangutan/2024-01-08/NHGRI/NIH
07	75.635	GCA_028878055.2	syntenic net	siamang/2024-01-05/NHGRI/NIH
08	59.789	GCF_011100555.1	maf net	white-tufted-ear marmoset/2021-04-28/VGP
09	28.119	GCF_020740605.2	maf net	Ring-tailed lemur/2021-11-04/VGP
10	13.212	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	lift over	common name	assembly
81.301	80.597	77.710	81.230	Human	hg38
81.201	80.601	77.815	81.160	Human	hs1
79.907	79.396	77.605	79.881	pygmy chimpanzee	GCA_029289425.2
79.878	79.391	77.625	79.854	chimpanzee	GCA_028858775.2
79.307	78.443	75.405	79.262	Sumatran orangutan	GCA_028885655.2
79.288	78.389	75.389	79.243	Bornean orangutan	GCA_028885625.2
75.635	74.621	71.272	75.585	siamang	GCA_028878055.2
59.789	58.571	56.557	59.715	white-tufted-ear marmoset	GCF_011100555.1
28.119	27.306	26.902	28.089	Ring-tailed lemur	GCF_020740605.2
13.212	12.423	12.621	13.189	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 western lowland gorilla//hive/data/genomes/asmHubs/genbankBuild/GCA/029/281/585/GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri/html/GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri.names.tab/GCA_029281585.2/2024-01-08 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.

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