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/worm/ce4/multiz5way.html src/hg/makeDb/trackDb/worm/ce4/multiz5way.html index 9ac1e3ed173..9d8e2cfe9d4 100644 --- src/hg/makeDb/trackDb/worm/ce4/multiz5way.html +++ src/hg/makeDb/trackDb/worm/ce4/multiz5way.html @@ -1,255 +1,282 @@ <H2>Description</H2> <P> <P> This track shows a measure of evolutionary conservation in <I>C. elegans, C. brenneri, C. remanei, C. briggsae</I> and <I>P. pacificus</I> based on a phylogenetic hidden Markov model, phastCons (Siepel <em>et al.</em>, 2005). Multiz alignments of the following assemblies were used to generate this track: <UL> <LI>$organism (WS170) ($date, $db) <LI>C. brenneri (Jan 2007, caePb1) <LI>C. remanei (Mar 2006, caeRem2) <LI>C. briggsae (Jan 2007, cb3) <LI>P. pacificus (Feb 2007, priPac1) </UL></P> <H2>Display Conventions and Configuration</H2> <P> In full and pack display modes, conservation scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. Pairwise alignments of each species to the <em>$organism</em> genome are displayed below 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> The conservation wiggle 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> Checkboxes in the track configuration section allow excluding species from the pairwise display; however, this does not remove them from the conservation score display. 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> <H3>Gap Annotation</H3> <P> The "Display chains between alignments" 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 <em>$organism</em> genome or a lineage-specific deletion between the aligned blocks in the aligning species. <LI><B>Double line:</B> Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. <LI><B>Pale yellow coloring:</B> Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. </UL></P> <H3>Genomic Breaks</H3> <P> Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: <UL> <LI> <B>Vertical blue bar:</B> Represents a discontinuity that persists indefinitely on either side, <em>e.g.</em> a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. <LI> <B>Green square brackets:</B> Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the <em>$organism</em> 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 <em>$organism</em> sequence at those alignment positions relative to the longest non-<em>$organism</em> 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.</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 to establish reading frame</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: <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>Worm Base Genes (Sanger Genes)</TD><TD>C. elegans</TD></TR> <TR ALIGN=left><TD>C. elegans mapped Genes</TD><TD>C. brenneri</TD></TR> <TR ALIGN=left><TD>C. elegans mapped Genes</TD><TD>C. remanei</TD></TR> <TR ALIGN=left><TD>C. elegans mapped Genes</TD><TD>C. briggsae</TD></TR> <TR ALIGN=left><TD>C. elegans mapped Genes</TD><TD>P. pacificus</TD></TR> </TABLE></BLOCKQUOTE> </P> <H2>Methods</H2> <P> Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, following the ordering of the species tree diagrammed above. These 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=ce4&hgta_group=compGeno&hgta_track=multiz5way">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=ce4">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/ce4/multiz5way/" + 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 by Scott Schwartz and Webb Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" 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 UCSC. <LI>"Wiggle track" plotting software by Hiram Clawson at UCSC. </UL> </P> <P>The phylogenetic tree is based on Kiontke and Fitch (2005). <H2>References</H2> <H3>Phylo-HMM:</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, 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> <P> Siepel A, Haussler D. <a href="https://repository.cshl.edu/id/eprint/31038/" target="_blank">Phylogenetic Hidden Markov Models</a>. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. </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. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/7713447" target="_blank">7713447</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1206396" target="_blank">PMC1206396</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>Blastz:</H3> <P> Chiaromonte F, Yap VB, Miller W. <A HREF="https://www.ncbi.nlm.nih.gov/pubmed/11928468/" 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> <H3>Phylogenetic Tree:</H3> <P> Kiontke K, Fitch DHA. <A HREF="http://www.wormbook.org/chapters/www_phylogrhabditids/phylorhab.html" TARGET=_blank>The phylogenetic relationships of <em>Caenorhabditis</em> and other rhabditids</A>. <em>WormBook</em>. 2005 Aug 11:1-11. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18050394" target="_blank">18050394</a> </p>