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/drosophila/netDp3.html src/hg/makeDb/trackDb/drosophila/netDp3.html index f1ecd22..251033e 100644 --- src/hg/makeDb/trackDb/drosophila/netDp3.html +++ src/hg/makeDb/trackDb/drosophila/netDp3.html @@ -1,95 +1,95 @@ <H2>Description</H2> <P> This track shows the best <em>$o_organism</em>/<em>$organism</em> chain for every part of the <em>$organism</em> genome. It is useful for finding orthologous regions and for studying genome rearrangement. The <em>$o_organism</em> sequence used in this annotation is from the $o_date ($o_db) assembly.</P> <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 dp3 data were obtained from the <A HREF="http://flybase.org/" TARGET=_blank>FlyBase</A> Release 1.0 assembly.</P> <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 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> <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>