src/hg/makeDb/trackDb/chainMm5.html 1.5

Index: src/hg/makeDb/trackDb/chainMm5.html
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RCS file: src/hg/makeDb/trackDb/chainMm5.html
diff -N src/hg/makeDb/trackDb/chainMm5.html
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-<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 $organism simultaneously. These 
-&quot;double-sided&quot; gaps can be caused by local inversions and 
-overlapping deletions in both species. 
-<P>
-The chain track displays boxes joined together by either single or
-double lines. The boxes represent aligning regions.
-Single lines indicate gaps that are largely due to a deletion in the
-$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 &quot;off&quot; 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 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. 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://bio.cse.psu.edu" 
-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>
-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="http://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>
-