Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (slow loris - 2022-12-28 - 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	37.596	GCF_020740605.2	maf net	Ring-tailed lemur/2021-11-04/VGP
02	16.270	GCA_028858775.2	maf net	chimpanzee/2024-01-08/NHGRI/NIH
03	16.268	GCA_029289425.2	maf net	pygmy chimpanzee/2024-01-08/NHGRI/NIH
04	16.254	hg38	maf net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
05	16.209	GCA_029281585.2	maf net	western lowland gorilla/2024-01-08/NHGRI/NIH
06	16.201	GCA_028885655.2	maf net	Sumatran orangutan/2024-01-05/NHGRI/NIH
07	16.197	GCA_028885625.2	maf net	Bornean orangutan/2024-01-08/NHGRI/NIH
08	16.154	hs1	maf net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
09	15.750	GCA_028878055.2	maf net	siamang/2024-01-05/NHGRI/NIH
10	12.281	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
37.596	36.346	35.844	37.550	Ring-tailed lemur	GCF_020740605.2
16.270	15.161	15.393	16.239	chimpanzee	GCA_028858775.2
16.268	15.144	15.394	16.238	pygmy chimpanzee	GCA_029289425.2
16.254	15.131	15.376	16.215	Human	hg38
16.209	15.089	15.332	16.175	western lowland gorilla	GCA_029281585.2
16.201	15.117	15.330	16.169	Sumatran orangutan	GCA_028885655.2
16.197	15.113	15.328	16.166	Bornean orangutan	GCA_028885625.2
16.154	15.048	15.281	16.123	Human	hs1
15.750	14.589	14.892	15.718	siamang	GCA_028878055.2
12.281	10.932	11.531	12.234	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 slow loris//hive/data/genomes/asmHubs/refseqBuild/GCF/027/406/575/GCF_027406575.1_mNycCou1.pri/html/GCF_027406575.1_mNycCou1.pri.names.tab/GCF_027406575.1/2022-12-28 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