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/medaka/oryLat2/phastConsElements5way.html src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html index 10eaddfb402..1f1b0e0ae14 100644 --- src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html +++ src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html @@ -1,108 +1,124 @@ <H2>Description</H2> <P> This track shows predictions of conserved elements produced by the phastCons program. PhastCons is part of the PHAST (PHylogenetic Analysis with Space/Time models) package. The predictions are based on a phylogenetic hidden Markov model (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. </P> <H2>Methods</H2> <P> Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting. A multiple alignment was then constructed from these pairwise alignments using multiz. Predictions of conserved elements were then obtained by running phastCons on the multiple alignments with the --most-conserved option.</P> <P> PhastCons constructs a two-state phylo-HMM with a state for conserved regions and a state for non-conserved regions. The two states share a single phylogenetic model, except that the branch lengths of the tree associated with the conserved state are multiplied by a constant scaling factor <em>rho</em> (0 <= <em>rho</em> <= 1). The free parameters of the phylo-HMM, including the scaling factor <em>rho</em>, are estimated from the data by maximum likelihood using an EM algorithm. This procedure is subject to certain constraints on the "coverage" of the genome by conserved elements and the "smoothness" of the conservation scores. Details can be found in Siepel et al. (2005).</P> <P> The predicted conserved elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".</P> +<h2>Data Access</h2> +<p> +The conserved elements can be retrieved for a single region or for a list of regions with the <a +href="hgTables?db=oryLat2&hgta_group=compGeno&hgta_track=phastConsElements5way">Table +Browser</a>, and joined with other annotations in the <a href="hgIntegrator?db=oryLat2">Data +Integrator</a>. For automated access, they are also served by our <a +href="../goldenPath/help/api.html">REST API</a>. +</p> +<p> +The files behind this track can be downloaded from our download server: +<ul> + <li><a href="https://hgdownload.soe.ucsc.edu/goldenPath/oryLat2/phastCons5way/" + target="_blank">PhastCons conservation scores and conserved elements</a></li> +</ul> +</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://www.ccbb.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. </UL> </P> <H2>References</H2> <H3>PhastCons</H3> <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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16024819" target="_blank">16024819</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182216/" target="_blank">PMC1182216</a> </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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a> </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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15060014" target="_blank">15060014</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383317/" target="_blank">PMC383317</a> </p> <H3>Blastz</H3> <p> Chiaromonte F, Yap VB, Miller W. <a href="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf" target="_blank">Scoring pairwise genomic sequence alignments</a>. <em>Pac Symp Biocomput</em>. 2002:115-26. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a> </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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a> </p>