7a820a27de93e79180f99ae0e149585b5d1bb126 mspeir Tue Dec 23 16:02:10 2025 -0800 adding better species coloring description to rest of conservation tracks, refs #27217 diff --git src/hg/makeDb/trackDb/human/hg18/multiz28way.html src/hg/makeDb/trackDb/human/hg18/multiz28way.html index 58651d01dda..a62b4370c99 100644 --- src/hg/makeDb/trackDb/human/hg18/multiz28way.html +++ src/hg/makeDb/trackDb/human/hg18/multiz28way.html @@ -1,441 +1,443 @@ <H2>Description</H2> <P> This track shows multiple alignments of 28 vertebrate species and two measures of evolutionary conservation -- conservation across all 28 species and an alternative measurement restricted to the placental mammal subset (17 species plus human) of the alignment. These two measurements produce the same results in regions where only mammals appear in the alignment. For other regions, the non-mammalian species can either boost the scores (if conserved) or decrease them (if non-conserved). The mammalian conservation helps to identify sequences that are under different evolutionary pressures in mammalian and non-mammalian vertebrates. </P> <P> The multiple alignments were generated using multiz and other tools in the UCSC/<A HREF="http://www.bx.psu.edu/miller_lab/" TARGET=_blank>Penn State Bioinformatics</A> comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from <A HREF="https://siepellab.labsites.cshl.edu/" TARGET=_blank> Adam Siepel</A> at Cold Spring Harbor Laboratory. </P> <P> The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 17-vertebrate alignment, this track includes 11 new species and 6 species with updated sequence assemblies (<B>Table 1</B>). The new species consist of five high-coverage (5-8.5X) assemblies (horse, platypus, lizard, and two teleost fish: stickleback and medaka) and six low-coverage (2X) genome assemblies from mammalian species selected for sampling by NHGRI (bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat). The chimp, cow, chicken, frog, fugu, and zebrafish assemblies in this track have been updated from those used in the previous 17-species alignment. </P> <P> UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the sequence for download; however, we do not construct genome browsers for them. Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see <EM>Gap Annotation</EM>, below). </P> <P> <BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa"> <TR ALIGN=left><TH>Organism</TH><TH>Species</TH><TH>Release date</TH><TH>UCSC version</TH></TR> <TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD> Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=hg18" TARGET=_blank>hg18</A></TD></TR> <TR ALIGN=left><TD>Armadillo</TD><TD>Dasypus novemcinctus</TD><TD>May 2005</TD> <TD> dasNov1</TD></TR> <TR ALIGN=left><TD>Bushbaby</TD><TD>Otolemur garnetti</TD><TD>Dec 2006</TD> <TD> otoGar1</TD></TR> <TR ALIGN=left><TD>Cat</TD><TD>Felis catus</TD><TD> Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=felCat3" TARGET=_blank>felCat3</A></TD></TR> <TR ALIGN=left><TD>Chicken</TD><TD>Gallus gallus</TD><TD> May 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=galGal3" TARGET=_blank>galGal3</A></TD></TR> <TR ALIGN=left><TD>Chimpanzee</TD><TD>Pan troglodytes</TD><TD> Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=panTro2" TARGET=_blank>panTro2</A></TD></TR> <TR ALIGN=left><TD>Cow</TD><TD>Bos taurus</TD> <TD>Aug 2006</TD><TD><A HREF="../cgi-bin/hgGateway?db=bosTau3" TARGET=_blank>bosTau3</A></TD></TR> <TR ALIGN=left><TD>Dog</TD><TD>Canis familiaris</TD><TD> May 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=canFam2" TARGET=_blank>canFam2</A></TD></TR> <TR ALIGN=left><TD>Elephant</TD><TD>Loxodonta africana</TD><TD>May 2005</TD> <TD> loxAfr1</TD></TR> <TR ALIGN=left><TD>Frog</TD><TD>Xenopus tropicalis</TD><TD> Aug 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=xenTro2" TARGET=_blank>xenTro2</A></TD></TR> <TR ALIGN=left><TD>Fugu</TD><TD>Takifugu rubripes</TD><TD> Oct 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=fr2" TARGET=_blank>fr2</A></TD></TR> <TR ALIGN=left><TD>Guinea pig</TD><TD>Cavia porcellus</TD><TD>Oct 2005</TD> <TD> cavPor2</TD></TR> <TR ALIGN=left><TD>Hedgehog</TD><TD>Erinaceus europaeus</TD><TD>June 2006</TD> <TD> eriEur1</TD></TR> <TR ALIGN=left><TD>Horse</TD><TD>Equus caballus</TD><TD> Feb 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=equCab1" TARGET=_blank>equCab1</A></TD></TR> <TR ALIGN=left><TD>Lizard</TD><TD>Anolis carolinensis</TD><TD> Feb 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=anoCar1" TARGET=_blank>anoCar1</A></TD></TR> <TR ALIGN=left><TD>Medaka</TD><TD>Oryzias latipes</TD><TD> Apr 2006</TD><TD>oryLat1</TD></TR> <TR ALIGN=left><TD>Mouse</TD><TD>Mus musculus</TD><TD> Feb 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=mm8" TARGET=_blank>mm8</A></TD></TR> <TR ALIGN=left><TD>Opossum</TD><TD>Monodelphis domestica</TD><TD> Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=monDom4" TARGET=_blank>monDom4</A></TD></TR> <TR ALIGN=left><TD>Platypus</TD><TD>Ornithorhychus anatinus</TD><TD> Mar 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=ornAna1" TARGET=_blank>ornAna1</A></TD></TR> <TR ALIGN=left><TD>Rabbit</TD><TD>Oryctolagus cuniculus</TD><TD>May 2005</TD> <TD> oryCun1</TD></TR> <TR ALIGN=left><TD>Rat</TD><TD>Rattus norvegicus</TD><TD> Nov 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rn4" TARGET=_blank>rn4</A></TD></TR> <TR ALIGN=left><TD>Rhesus</TD><TD>Macaca mulatta</TD><TD> Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rheMac2" TARGET=_blank>rheMac2</A></TD></TR> <TR ALIGN=left><TD>Shrew</TD><TD>Sorex araneus</TD><TD>June 2006</TD> <TD> sorAra1</TD></TR> <TR ALIGN=left><TD>Stickleback</TD><TD>Gasterosteus aculeatus</TD><TD> Feb 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=gasAcu1" TARGET=_blank>gasAcu1</A></TD></TR> <TR ALIGN=left><TD>Tenrec</TD><TD>Echinops telfairi</TD><TD>July 2005</TD> <TD> echTel1</TD></TR> <TR ALIGN=left><TD>Tetraodon</TD><TD>Tetraodon nigroviridis</TD><TD> Feb 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=tetNig1" TARGET=_blank>tetNig1</A></TD></TR> <TR ALIGN=left><TD>Tree shrew</TD><TD>Tupaia belangeri</TD><TD>Dec 2006</TD> <TD> tupBel1</TD></TR> <TR ALIGN=left><TD>Zebrafish</TD><TD>Danio rerio</TD><TD> Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=danRer4" TARGET=_blank>danRer4</A></TD></TR> </TABLE><BR> <B>Table 1.</B> <EM>Genome assemblies included in the 28-way Conservation track.</EM> </BLOCKQUOTE></P> <H2>Display Conventions and Configuration</H2> <P> The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a <EM>wiggle track</EM> (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 <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" TARGET=_blank>Graph configuration help</A> link for an explanation of the configuration options.</P> <P> Pairwise alignments of each species to the $organism 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. </P> <P> Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. +The names of selected species are colored according to their clade, +alternating between blue and green. Configuration buttons are available to select all of the species (<EM>Set all</EM>), deselect all of the species (<EM>Clear all</EM>), or use the default settings (<EM>Set defaults</EM>). By default, the following 11 species are included in the pairwise display: rhesus, mouse, dog, horse, armadillo, opossum, platypus, lizard, chicken, <EM>X. tropicalis</EM> (frog), and stickleback. Note that excluding species from the pairwise display does not alter the the conservation score display.</P> <P> 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.</P> <H3>Gap Annotation</H3> <P> The <EM>Display chains between alignments</EM> configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: <UL> <LI><B>Single line:</B> no bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the $organism genome or a lineage-specific deletion between the aligned blocks in the aligning species. <LI><B>Double line:</B> 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. <LI><B>Pale yellow coloring:</B> 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. </UL></P> <H3>Genomic Breaks</H3> <P> Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: <UL> <LI> <B>Vertical blue bar:</B> represents a discontinuity that persists indefinitely on either side, <em>e.g.</em> 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. <LI> <B>Green square brackets:</B> 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 $organism genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. </UL></P> <H3>Base Level</H3> <P> 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 $organism sequence at those alignment positions relative to the longest non-$organism 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 "+".</P> <P> Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: <UL> <LI> <B>No codon translation:</B> the gene annotation is not used; the bases are displayed without translation. <LI> <B>Use default species reading frames for translation:</B> the annotations from the genome displayed in the <EM>Default species for translation</EM>; pull-down menu are used to translate all the aligned species present in the alignment. <LI> <B>Use reading frames for species if available, otherwise no translation:</B> codon translation is performed only for those species where the region is annotated as protein coding. <LI><B>Use reading frames for species if available, otherwise use default species:</B> codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. </UL></P> <P> Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (<B>Table 2</B>). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation. <BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa"> <TR ALIGN=left><TD><B>Gene Track</B></TD><TD><B>Species</B></TD></TR> <TR ALIGN=left><TD>Known Genes</TD><TD>human, mouse, rat</TD></TR> <TR ALIGN=left><TD>RefSeq Genes</TD><TD>chimp</TD></TR> <TR ALIGN=left><TD>Ensembl Genes</TD><TD>rhesus, opossum, zebrafish, fugu, stickleback</TD></TR> <TR ALIGN=left><TD>mRNAs</TD><TD>rabbit, dog, cow, horse, chicken, frog, tetraodon</TD></TR> <TR ALIGN=left><TD>None</TD><TD>bushbaby, tree shrew, guinea pig, rabbit, shrew, hedgehog,<BR> cat, armadillo, elephant, tenrec, platypus, lizard, medaka</TD></TR> </TABLE> <B>Table 2.</B> <EM>Gene tracks used for codon translation.</EM> </BLOCKQUOTE></P> <H2>Methods</H2> <P> Pairwise alignments with the human genome were generated for each species using blastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.</P> <P> An additional filtering step was introduced in the generation of the 28-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best").</P> <P> The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/multiz28way" TARGET=_blank>bulk download</A>. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.</P> <P> Conservation scoring was performed using the PhastCons package (A. Siepel), which computes conservation based on a two-state phylogenetic hidden Markov model (HMM). PhastCons measurements rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons28way/28way.mod" TARGET=_blank>vertebrate tree model</A> for this track was generated using the phyloFit program from the phastCons package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 28way alignment (msa_view). The 4d sites were derived from the <A HREF="https://genome.crg.es/gencode/" TARGET=_blank>Oct 2005 Gencode Reference Gene set</A>, which was filtered to select single-coverage long transcripts. A second, <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons28way/placental.mod" TARGET=_blank>mammalian tree model</A> including only placental mammals was used to generate the placental mammal conservation scoring. The phastCons parameters were tuned to produce 5% conserved elements in the genome for the vertebrate conservation measurement. This parameter set (expected-length=45, target-coverage=.3, rho=.31) was then used to generate the placental mammal conservation scoring.</P> <P> The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel <EM>et al</EM>. 2005.</P> <P> PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.</P> <H2>Credits</H2> <P> This track was created using the following programs: <UL> <LI> Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" TARGET=_blank>Penn State Bioinformatics Group</A> <LI> Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC <LI> Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by <A HREF="https://siepellab.labsites.cshl.edu/" TARGET=_blank>Adam Siepel</A> while at UCSC, now at Cold Spring Harbor Laboratory <LI> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC <LI> Tree image generator: phyloPng by Galt Barber, UCSC <LI> Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC </UL> </P> <P>The phylogenetic tree is based on Murphy <EM>et al</EM>. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. </P> <H2>References</H2> <H3>Phylo-HMMs and phastCons:</H3> <P> Felsenstein J, Churchill GA. <A HREF="https://academic.oup.com/mbe/article/13/1/93/1055515" TARGET=_blank>A Hidden Markov Model approach to variation among sites in rate of evolution</A>. <EM>Mol Biol Evol</EM>. 1996 Jan;13(1):93-104. </P> <P> Siepel A, Haussler D. <A HREF="http://compgen.cshl.edu/~acs/phylohmm.pdf" TARGET=_blank>Phylogenetic Hidden Markov Models</A>. In R. Nielsen, ed., <em>Statistical Methods in Molecular Evolution</em>, pp. 325-351, Springer, New York (2005). </P> <P> Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, <EM>et al.</EM> <A HREF="https://genome.cshlp.org/content/15/8/1034" TARGET=_blank>Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes</A>. <EM>Genome Res</EM>. 2005 Aug;15(8):1034-50. </P> <P> Yang Z. <A HREF="https://www.genetics.org/content/139/2/993" TARGET=_blank>A space-time process model for the evolution of DNA sequences</A>. <EM>Genetics</EM>. 1995 Feb;139(2):993-1005. </P> <H3>Chain/Net:</H3> <P> Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. <A HREF="https://www.pnas.org/content/100/20/11484" TARGET=_blank>Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</A>. <EM>Proc Natl Acad Sci U S A</EM>. 2003 Sep 30;100(20):11484-9. </P> <H3>Multiz:</H3> <P> Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, <EM>et al.</EM> <A HREF="https://genome.cshlp.org/content/14/4/708.abstract" TARGET=_blank>Aligning multiple genomic sequences with the threaded blockset aligner</A>. <EM>Genome Res</EM>. 2004 Apr;14(4):708-15. </P> <H3>Blastz:</H3> <P> Chiaromonte F, Yap VB, Miller W. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928468&dopt=Abstract" TARGET=_blank>Scoring pairwise genomic sequence alignments</A>. <EM>Pac Symp Biocomput</EM>. 2002;:115-26. </P> <P> Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. <A HREF="https://genome.cshlp.org/content/13/1/103.abstract" TARGET=_blank>Human-mouse alignments with BLASTZ</A>. <EM>Genome Res</EM>. 2003 Jan;13(1):103-7. </P> <H3>Phylogenetic Tree:</H3> <P> Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. <A HREF="https://science.sciencemag.org/content/294/5550/2348" TARGET=_blank>Resolution of the early placental mammal radiation using Bayesian phylogenetics</A>. <EM>Science</EM>. 2001 Dec 14;294(5550):2348-51. </P>