efebc8a0a29aeef60bc470a40ced7a2aa6652efd
lrnassar
  Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308

New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.

Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.

Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.

Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.html src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.html
new file mode 100644
index 00000000000..5241d10ddc6
--- /dev/null
+++ src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.html
@@ -0,0 +1,236 @@
+<h2>Description</h2>
+
+<p>
+Inbred laboratory mouse strains descend from a small pool of founder animals, so any two
+strains differ at millions of sites and carry long stretches of distinct ancestral haplotype.
+The Mouse Genomes Project built de novo assemblies for 16 of them, 12 classical laboratory
+strains and 4 derived from wild mice, covering most of the genetic diversity in common
+laboratory use. Seven of the eight Collaborative Cross and Diversity Outbred founder strains
+are included; the eighth, C57BL/6J, is the reference assembly itself.
+</p>
+
+<p>
+This track shows a whole-genome multiple alignment of those 16 strain assemblies to the
+mouse reference, with the rat genome included as an outgroup. It was built with Progressive
+Cactus from the assemblies themselves rather than by mapping short reads, so insertions and
+deletions in a strain appear directly in the alignment. Large rearrangements are a different
+matter: the strain scaffolds were joined into chromosomes using the reference as a guide and
+adjacencies that disagreed with it were mostly discarded, so this is not a good source for
+translocations or inversions.
+</p>
+
+<p>
+Note that the assembly included here is C57BL/6NJ, a substrain of the C57BL/6J animal the
+mouse reference was built from, so that row is nearly identical to the reference along most
+of the genome.
+</p>
+
+<p>
+The alignment is symmetric, so it can also be viewed with any of the 16 strains as the
+reference instead of C57BL/6J. To do that, load the
+<a href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html" target="_blank">Mouse
+strain assemblies</a> hub, which is on our public hub list, and pick a strain assembly from
+its gateway page.
+</p>
+
+<h2>Display Convention and Configuration</h2>
+
+<p>
+Each aligned assembly is shown on its own row, labeled with the strain name. The track
+configuration page lets you choose which assemblies to display. The strains are listed there
+in three groups, wild-derived, classical laboratory, and rat, each with a pair of buttons
+that turn the whole group on or off at once.
+</p>
+
+<p>
+To see the aligned bases at a given position, zoom in to 30,000 bases or fewer and click
+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 a manner similar to the Chain track display. Missing sequence
+in any assembly is highlighted by regions of yellow when zoomed out and by Ns at base
+level. The conventions are:
+</p>
+<ul>
+  <li><b>Single line:</b> no bases in the aligned assembly. Possibly a strain-specific
+      insertion between the aligned blocks in the reference, or a strain-specific deletion
+      between the aligned blocks in the other assembly.</li>
+  <li><b>Double line:</b> the aligned assembly has one or more unalignable bases in the gap
+      region, which can happen with independent indels in the region between the aligned
+      blocks in both assemblies.</li>
+  <li><b>Pale yellow coloring:</b> the aligned assembly has Ns in the gap region, reflecting
+      a lack of sequence in the relevant portion of that assembly.</li>
+</ul>
+
+<h3>Genomic Breaks</h3>
+<p>
+Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA
+are shown as follows:
+</p>
+<ul>
+  <li><b>Vertical blue bar:</b> a discontinuity that persists indefinitely on either side,
+      for example a large region of DNA on either side of the bar coming from a different
+      chromosome in the aligned assembly because of a large scale rearrangement.</li>
+  <li><b>Green square brackets:</b> enclose shorter alignments consisting of DNA from one
+      genomic context nested inside a larger chain of alignments from a different genomic
+      context. The alignment within the brackets may represent a short misalignment, a
+      strain-specific transposon insertion that aligns to a paralogous copy elsewhere, or a
+      similar occurrence.</li>
+</ul>
+
+<h3>Base Level</h3>
+<p>
+When zoomed in to base 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 reference sequence
+at those alignment positions, relative to the longest non-reference 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 at base level when the displayed region is annotated as
+coding. To turn it on, pick a species in the Codon Translation section of the configuration
+page and then choose one of these modes:
+</p>
+<ul>
+  <li><b>No codon translation:</b> the gene annotation is not used; bases are displayed
+      without translation.</li>
+  <li><b>Use default species reading frames for translation:</b> the annotations from the
+      assembly chosen in the <em>Default species to establish reading frame</em> menu are
+      used to translate all aligned assemblies.</li>
+  <li><b>Use reading frames for species if available, otherwise no translation:</b> codon
+      translation is done only for assemblies where the region is annotated as protein
+      coding.</li>
+  <li><b>Use reading frames for species if available, otherwise use default species:</b>
+      assemblies annotated as protein coding over the aligned region are translated with
+      their own annotation; the rest are translated using the default assembly.</li>
+</ul>
+
+<h2>Methods</h2>
+
+<p>
+The 16 strain assemblies were produced by the Mouse Genomes Project at the Wellcome Sanger
+Institute from Illumina paired-end reads at 40x to 70x coverage, mate-pair libraries at 3, 6
+and 10 kb, and fosmid and BAC-end sequences. CAST/EiJ, PWK/PhJ and SPRET/EiJ were scaffolded
+further with Dovetail Genomics Chicago libraries through HiRise. Scaffolds were then joined
+into chromosome-scale sequences with Ragout v2.0, using the C57BL/6J GRCm38 sequence as the
+single reference and minimizing the number of structural differences from it. On average 10%
+of synteny block adjacencies in the assemblies were absent from the reference; Ragout kept
+the 38% of those it judged to be real rearrangements and removed the remainder as
+mis-assemblies. The GenBank version of each assembly was used here. A Progressive Cactus
+alignment was then generated
+from those 16 assemblies together with the mouse reference (mm10) and the rat reference
+(rn6), giving 18 genomes in total. Because the laboratory strains are so closely related,
+the Cactus guide tree was binarized as accurately as possible, but incomplete lineage
+sorting is common among these strains and the guide tree may not be correct in every region.
+This has little effect on alignment quality except where insertions and deletions themselves
+fall under incomplete lineage sorting. The guide tree is shown on the track configuration
+page. See the references below for details of both the assemblies and the alignment method.
+</p>
+
+<p>
+The alignment is served directly from the files behind the
+<a href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/" target="_blank">mouse strains
+assembly hub</a> on our download server, at
+<a href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/" target="_blank">https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/</a>.
+No reprocessing was done for this track; only the track configuration differs from the hub.
+The full alignment is also available in HAL format as
+<a href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mouseStrains_1509.hal" target="_blank">mouseStrains_1509.hal</a>,
+and the bigMaf files displayed here were generated from it.
+</p>
+
+<p>
+The steps taken to add this track are recorded in
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/mm10/mouseStrainsCactus.txt" target="_blank">doc/mm10/mouseStrainsCactus.txt</a>,
+and its track configuration is in
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.ra" target="_blank">trackDb/mouse/mm10/mouseStrainsCactus.ra</a>.
+</p>
+
+<h2>Data Access</h2>
+
+<p>
+The alignment can be explored interactively with the
+<a href="../cgi-bin/hgTables">Table Browser</a>, which returns one MAF block per row. From
+scripts, the data can be accessed through our
+<a href="https://api.genome.ucsc.edu" target="_blank">API</a>,
+track=<i>mouseStrainsCactus</i>.
+</p>
+
+<p>
+For automated download and analysis, the alignment is stored in bigMaf format and can be
+downloaded from
+<a href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/" target="_blank">our
+download server</a>. The files are called <tt>mm10.bigMaf.bb</tt> (the alignment, roughly 9 GB),
+<tt>mm10.bigMafSummary.bb</tt> (the zoomed-out summary) and <tt>mm10.bigMafFrames.bb</tt>
+(the coding frames used for codon translation). Individual regions or the whole alignment
+can be converted to MAF with our tool <tt>bigMafToMaf</tt>, which can be compiled from the
+source code or downloaded as a precompiled binary for your system. Instructions for
+downloading source code and binaries can be found
+<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
+The tool reads the file over the network, so a single region can be pulled out without
+downloading the whole alignment:
+</p>
+<pre>
+bigMafToMaf https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/mm10.bigMaf.bb \
+    region.maf -chrom=chr1 -start=3000000 -end=3100000
+</pre>
+
+<p>
+The 16 strain assemblies themselves can be downloaded from
+<a href="https://ftp.ebi.ac.uk/pub/databases/mousegenomes/" target="_blank">the Mouse Genomes
+Project archive at EMBL-EBI</a>.
+</p>
+
+<h2>Credits</h2>
+
+<p>
+Alignment generation: Joel Armstrong, Ian Fiddes and Benedict Paten, UC Santa Cruz Genomics
+Institute. Genome assemblies: Thomas Keane and the Mouse Genomes Project, Wellcome Sanger
+Institute.
+</p>
+
+<h2>References</h2>
+
+<p>
+Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S,
+Czechanski A <em>et al</em>.
+<a href="https://doi.org/10.1038/s41588-018-0223-8" target="_blank">
+Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel
+functional loci</a>.
+<em>Nat Genet</em>. 2018 Nov;50(11):1574-1583.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30275530" target="_blank">30275530</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205630/" target="_blank">PMC6205630</a>
+</p>
+
+<p>
+Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.
+<a href="https://genome.cshlp.org/lookup/pmidlookup?view=long&amp;pmid=21665927" target="_blank">
+Cactus: Algorithms for genome multiple sequence alignment</a>.
+<em>Genome Res</em>. 2011 Sep;21(9):1512-28.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21665927" target="_blank">21665927</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166836/" target="_blank">PMC3166836</a>
+</p>
+
+<p>
+Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
+<a href="https://www.ncbi.nlm.nih.gov/pubmed/23505295" target="_blank">
+HAL: a hierarchical format for storing and analyzing multiple genome alignments</a>.
+<em>Bioinformatics</em>. 2013 May 15;29(10):1341-2.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23505295" target="_blank">23505295</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707/" target="_blank">PMC3654707</a>
+</p>
+
+<p>
+Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D,
+Paten B.
+<a href="https://www.ncbi.nlm.nih.gov/pubmed/25138168" target="_blank">
+Comparative assembly hubs: web-accessible browsers for comparative genomics</a>.
+<em>Bioinformatics</em>. 2014 Dec 1;30(23):3293-301.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25138168" target="_blank">25138168</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/" target="_blank">PMC4296145</a>
+</p>
+