src/hg/makeDb/trackDb/chainHg19.html 1.1
1.1 2009/04/27 18:16:32 hiram
For chains and nets of Hg19 on other organisms
Index: src/hg/makeDb/trackDb/chainHg19.html
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RCS file: src/hg/makeDb/trackDb/chainHg19.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 $organism simultaneously. These
+"double-sided" gaps can be caused by local inversions and
+overlapping deletions in both species.
+<P>
+The chain track displays boxes joined together by either single or
+double lines. The boxes represent aligning regions.
+Single lines indicate gaps that are largely due to a deletion in the
+$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 "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 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://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 VB, 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.</em> 2002;:115-26.</P>
+<P>
+Kent WJ, Baertsch R, Hinrichs A, Miller W, 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 U S A</em>. 2003 Sep 30;100(20):11484-9.</P>
+<P>
+Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
+Haussler D, 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> 2003 Jan;13(1):103-7.</P>
+