8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/mouseNet.html src/hg/makeDb/trackDb/mouseNet.html index 7fffd7c..19ac8aa 100644 --- src/hg/makeDb/trackDb/mouseNet.html +++ src/hg/makeDb/trackDb/mouseNet.html @@ -1,87 +1,87 @@ <H2>Description</H3> <P> This track shows the best mouse/$organism chain for every part of the $organism genome. It is useful for finding orthologous regions and for studying genome rearrangement. <H2>Display Conventions and Configuration</H2> <P> In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. </P> <P> In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. </P> <P> Individual items in the display are categorized as one of four types (other than gap):</P> <P><UL> <LI><B>Top</B> - the best, longest match. Displayed on level 1. <LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above it. <LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in the opposite orientation. <LI><B>NonSyn</B> - a match to a chromosome different from the gap in the level above. </UL></P> <H2>Methods</H2> <P> Chains were derived from blastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained <em>N</em>s (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.</P> <H2>Credits</H2> <P> The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.</P> <P> Blastz was developed at <A HREF="http://www.bx.psu.edu/miller_lab" TARGET=_blank>Pennsylvania State University</A> by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.</P> <P> Lineage-specific repeats were identified by Arian Smit and his program -<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>.</P> +<A HREF="https://www.repeatmasker.org/" TARGET=_blank>RepeatMasker</A>.</P> <P> The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.</P> <H2>References</H2> <P> Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. <A HREF="http://www.pnas.org/cgi/content/abstract/1932072100v1" TARGET=_blank>Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes</A>. <em>Proc Natl Acad Sci USA</em> <B>100</B>(20), 11484-11489 (2003).</P> <P> Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. <A HREF="http://www.genome.org/cgi/content/abstract/13/1/103" TARGET=_blank>Human-Mouse Alignments with BLASTZ</A>. <em>Genome Res.</em> <B>13</B>(1), 103-7 (2003).</P>