97805fb2ceb73357aa78aa94107148dc355d4e1c mspeir Tue Sep 22 08:36:22 2026 -0700 Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html index f68a9b882b3..6322be8d71e 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html +++ src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html @@ -1,155 +1,182 @@ <H2>Description</H2> <P> This track shows a measure of evolutionary conservation in $organism, Tetraodon, Fugu, mouse, human and opossum based on a phylogenetic hidden Markov model (phastCons). Multiz alignments of the following assemblies were used to generate this annotation: <UL> <LI>$organism ($date, $db) <LI>Tetraodon (Feb. 2004, tetNig1) <LI>Fugu (Aug. 2002, fr1) <LI>human (May 2004, hg17) <LI>mouse (Mar. 2005, mm6) <LI>opossum (Oct. 2004, monDom1) </UL></P> <H2>Display Conventions and Configuration</H2> <P> <P> In full display mode, this track shows the overall conservation score across all species, as well as pairwise alignments of human, mouse, opossum, Fugu and Tetraodon each aligned to the $organism genome. The pairwise alignments are shown in dense display mode using a grayscale density gradient. The checkboxes in the track configuration section allow the exclusion of species from the pairwise display; however, this does not remove them from the conservation score display. </P> <P> When zoomed-in to the base-display level, 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 not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown. To view detailed information about the alignments at a specific position, zoom in the display to 30,000 or fewer bases, then click on the alignment.</P> <P> This track may 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> <H2>Methods</H2> <P> Best-in-genome blastz pairwise alignments were multiply aligned using multiz, beginning with $organism-human alignments and subsequently adding in mouse and opossum. This was added to an alignment of $organism-Tetraodon aligned to Fugu. The resulting multiple alignments were then assigned conservation scores by phastCons.</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. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (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>Data Access</h2> +<p> +The alignments and the conservation scores can be retrieved for a single region or for a list of +regions with the <a +href="hgTables?db=danRer2&hgta_group=compGeno&hgta_track=multiz6way">Table Browser</a>, +which returns the alignments in MAF format and the scores as wiggle data. The conservation +scores, though not the alignments, can also be joined with other annotations in the <a +href="hgIntegrator?db=danRer2">Data Integrator</a>. For automated access, our <a +href="../goldenPath/help/api.html">REST API</a> serves the alignment and conservation tracks +individually, by name. +</p> +<p> +The files behind this track can be downloaded from our download server: +<ul> + <li><a href="https://hgdownload.soe.ucsc.edu/goldenPath/danRer2/multiz6way/" + target="_blank">Multiz alignments and phylogenetic trees</a></li> +</ul> +</p> +<p> +Genome-wide alignment files are large. Among our command-line programs, <tt>mafsInRegion</tt>, +<tt>mafSpeciesSubset</tt> and <tt>mafFrags</tt> pull out a region, a subset of species, or the +alignment underlying a gene. They can be downloaded from the <a +href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">utilities directory</a>, and +each one prints its usage when run with no arguments. See our <a +href="../FAQ/FAQdownloads.html">Data Access FAQ</a> for more information. +</p> + <H2>Credits</H2> <P> This track was created at UCSC using the following programs: <UL> <LI> Blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the <A HREF="http://bio.cse.psu.edu/" TARGET=_blank>Penn State Bioinformatics Group</A>. <LI> AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC. <LI> PhastCons by Adam Siepel at Cornell University. <LI>"Wiggle track" plotting software by Hiram Clawson at UCSC. </UL> </P> <P>The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community. </P> <H2>References</H2> <H3>Phylo-HMMs and phastCons</H3> <P> Felsenstein J and Churchill GA (1996). <A HREF="http://mbe.oxfordjournals.org/cgi/content/abstract/13/1/93" TARGET=_blank>A hidden Markov model approach to variation among sites in rate of evolution</A>. <em>Mol Biol Evol</em> 13:93-104. </P> <P> Siepel A and Haussler D (2005). Phylogenetic hidden Markov models. In R. Nielsen, ed., <em>Statistical Methods in Molecular Evolution</em>, pp. 325-351, Springer, New York. </P> <P> Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. <A HREF="http://www.genome.org/cgi/doi/10.1101/gr.3715005" TARGET=_blank>Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes</A>. <em>Genome Res.</em> <B>15</B>, 1034-1050 (2005).</P> <P> Yang Z (1995). <A HREF="http://www.genetics.org/cgi/content/abstract/139/2/993" TARGET=_blank>A space-time process model for the evolution of DNA sequences</A>. <em>Genetics</em>, 139:993-1005. </P> <H3>Chain/Net</H3> <P> Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. <A HREF="http://www.pnas.org/cgi/content/abstract/1932072100v1" TARGET=_blank>Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes</A>. <em>Proc Natl Acad Sci USA</em> <B>100</B>(20), 11484-11489 (2003).</P> <H3>Multiz</H3> <P> Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W. <A HREF="http://www.genome.org/cgi/content/abstract/14/4/708" TARGET=_blank>Aligning multiple genomic sequences with the threaded blockset aligner</A>. <em>Genome Res.</em> <B>14</B>(4), 708-15 (2004).</P> <H3>Blastz</H3> <P> Chiaromonte, F., Yap, V.B., 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 2002</em>, 115-26 (2002).</P> <P> Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. <A HREF="http://www.genome.org/cgi/content/abstract/13/1/103" TARGET=_blank>Human-Mouse Alignments with BLASTZ</A>. <em>Genome Res.</em> <B>13</B>(1), 103-7 (2003).</P> <H3>Phylogenetic Tree</H3> <P> Murphy, W.J., et al. <A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5550/2348" TARGET=_blank>Resolution of the early placental mammal radiation using Bayesian phylogenetics</A>. <em>Science</em> <B>294</B>(5550), 2348-51 (2001).</P>