Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (Ring-tailed lemur - 2021-11-04 - Vertebrate Genomes Project).

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	47.884	GCF_027406575.1	maf net	slow loris/2022-12-28/VGP
02	43.366	GCA_028858775.2	maf net	chimpanzee/2024-01-08/NHGRI/NIH
03	43.364	GCA_029289425.2	maf net	pygmy chimpanzee/2024-01-08/NHGRI/NIH
04	43.348	hg38	maf net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
05	43.347	hs1	maf net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
06	43.286	GCA_028885655.2	maf net	Sumatran orangutan/2024-01-05/NHGRI/NIH
07	43.272	GCA_028885625.2	maf net	Bornean orangutan/2024-01-08/NHGRI/NIH
08	43.269	GCA_029281585.2	maf net	western lowland gorilla/2024-01-08/NHGRI/NIH
09	41.960	GCA_028878055.2	maf net	siamang/2024-01-05/NHGRI/NIH
10	32.460	GCF_011100555.1	maf net	white-tufted-ear marmoset/2021-04-28/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
47.884	46.715	46.538	47.786	slow loris	GCF_027406575.1
43.366	42.715	42.561	43.310	chimpanzee	GCA_028858775.2
43.364	42.711	42.560	43.307	pygmy chimpanzee	GCA_029289425.2
43.348	42.672	42.532	43.278	Human	hg38
43.347	42.695	42.544	43.292	Human	hs1
43.286	42.626	42.483	43.228	Sumatran orangutan	GCA_028885655.2
43.272	42.615	42.472	43.214	Bornean orangutan	GCA_028885625.2
43.269	42.616	42.466	43.212	western lowland gorilla	GCA_029281585.2
41.960	41.319	41.183	41.912	siamang	GCA_028878055.2
32.460	31.766	31.869	32.416	white-tufted-ear marmoset	GCF_011100555.1

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 Ring-tailed lemur//hive/data/genomes/asmHubs/refseqBuild/GCF/020/740/605/GCF_020740605.2_mLemCat1.pri/html/GCF_020740605.2_mLemCat1.pri.names.tab/GCF_020740605.2/2021-11-04 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