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/marmoset/calJac3/cons13way.html src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html index fb5b811a3ce..63d24d415c8 100644 --- src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html +++ src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html @@ -149,40 +149,30 @@ <tr> <td>Opossum</td> <td>Monodelphis domestica</td> <td>Oct. 2006</td> <td><a href="../cgi-bin/hgGateway?db=monDom5" target="_blank">monDom5</a></td> <td>Syntenic Net</td> </tr> </table> <BR> <B>Table 1.</B> <EM>Genome assemblies included in the 13-way Conservation track.</EM> <BR>* Data download only, browser not available. </BLOCKQUOTE> -Downloads for data in this track are available: -<UL> -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/calJac3/multiz13way/">Multiz alignments</A> (MAF format), and phylogenetic trees <LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/calJac3/phyloP13way/">PhyloP conservation</A> (WIG format) -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/calJac3/phastCons13way/">PhastCons conservation</A> (WIG format) -</UL> - - <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 @@ -362,30 +352,60 @@ 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>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=calJac3&hgta_group=compGeno&hgta_track=cons13way">Table Browser</a>, +which returns the alignments in MAF format and the scores as wiggle data. The scores and the +conserved elements, though not the alignments, can also be joined with other annotations in the +<a href="hgIntegrator?db=calJac3">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> +Downloads for data in this track are available: +<UL> +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/calJac3/multiz13way/" target="_blank">Multiz alignments</A> (MAF format), and phylogenetic trees <LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/calJac3/phyloP13way/" target="_blank">PhyloP conservation</A> (WIG format) +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/calJac3/phastCons13way/" target="_blank">PhastCons conservation</A> (WIG format) +</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 using the following programs: <UL> <LI> Alignment tools: lastz (formerly 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