e435de108aa1574d959ee3fbc40d674f1bf49224 jcasper Mon Aug 26 15:32:43 2024 -0700 Replacing references to hgwdev.soe.ucsc.edu, as that server name is deprecated. no ticket diff --git src/hg/makeDb/trackDb/mouseStrains.html src/hg/makeDb/trackDb/mouseStrains.html index a1c7391..31e6142 100644 --- src/hg/makeDb/trackDb/mouseStrains.html +++ src/hg/makeDb/trackDb/mouseStrains.html @@ -34,31 +34,31 @@ </p> <h2>Methods</h2> <p> A <em>snake</em> is a way of viewing a set of pairwise gap-less alignments that may overlap on both the reference and query genomes. Alignments are always represented as being on the positive strand of the reference species, but can be on either strand on the query sequence. </p> <p> A <em>snake</em> plot puts all the query segments within a reference chromosome range on a set of one or more levels. All the segments on a level are on the same strand, do not overlap in reference coordinate space, and are in the same order and orientation in both sequences. This is the same requirement as the alignments in a chain on the UCSC browser. Before the algorithm is started, all the segments are sorted by their starting coordinate on the query, and the current level is set to one. Then in a recursive fashion, the algorithm places the first segment on the current list on the current level, and then adds all the rest of the segments on the list that will fit onto the current level with the requirements that all the segments on a level are on the same strand, and that the proposed segment be non-overlapping and have a reference start address that is greater than the query end address of the previously added segment on that level. All segments that will not fit on the current level are then added to subsequent levels following the same rules. Once all the segments have been assigned a level, lines are drawn between the segments to show the adjacencies in the list when sorted by query start address. </p> <p> For this assembly hub, a progressiveCactus alignment was generated using the Genbank version of these assemblies. The reference mouse (mm10) as well as the reference rat (rn6) were included as well. Here is the guide tree for this alignment: <p> -<img src="http://hgwdev.soe.ucsc.edu/~ifiddes/mouse_genomes_data/mouse_tree.png" alt="Mouse Genomes Phylogeny" height="600"> +<img src="http://hgwdev.gi.ucsc.edu/~ifiddes/mouse_genomes_data/mouse_tree.png" alt="Mouse Genomes Phylogeny" height="600"> </p> Due to the highly similar nature of the laboratory mice strains, this tree was binarized as well as possible, but incomplete lineage sorting is prevalent and as a result the guide tree may not be correct in all regions. </p> <h2>Credits</h2> <p> The <em>snake</em> alignment display was implemented by <a href="mailto:braney@soe. ucsc. edu"> braney@soe. ucsc. edu</a>.<br> <!-- above address is braney at soe.ucsc.edu -->