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/chain.html src/hg/makeDb/trackDb/chain.html index 3b2d42d..fce689c 100644 --- src/hg/makeDb/trackDb/chain.html +++ src/hg/makeDb/trackDb/chain.html @@ -1,86 +1,86 @@ <H2>Description</H2> <P> This track shows alignments of $o_organism ($o_db, $o_date) to the $organism genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both $o_organism and $organism simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. </P> <P> The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the $o_organism assembly or an insertion in the $organism assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the $organism genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. </P> <P> In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.</P> <H2>Display Conventions and Configuration</H2> <P>By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.</P> <P> To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.</P> <H2>Methods</H2> <P> Transposons that have been inserted since the $o_organism/$organism split were removed from the assemblies. The abbreviated genomes were aligned with blastz, and the transposons were then added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single $o_organism chromosome and a single $organism chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. $matrix Chains scoring below a threshold were discarded; the remaining chains are displayed in this track.</P> <H2>Credits</H2> <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 -<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A> +<A HREF="https://www.repeatmasker.org/" TARGET=_blank>RepeatMasker</A> program.</P> <P> The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. </P> <P> The browser display and database storage of the chains were generated by Robert Baertsch and Jim Kent.</P> <H2>References</H2> <P> Chiaromonte, F., Yap, V.B., Miller, W. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928468&dopt=Abstract" TARGET=_blank>Scoring pairwise genomic sequence alignments</A>. <em>Pac Symp Biocomput 2002</em>, 115-26 (2002).</P> <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>