src/hg/makeDb/trackDb/humanChainNet.html 1.1
1.1 2009/06/02 21:15:47 hiram
Adding hg19 chain and net composite track
Index: src/hg/makeDb/trackDb/humanChainNet.html
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+<H2>Description</H2>
+<H3>Chain Track</H3>
+<P>
+The chain track shows alignments of human (Feb. 2009/hg19) 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
+human 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
+human 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 $organism genome, the chains with single-lined gaps are often
+due to processed pseudogenes, while chains with double-lined gaps are more
+often due to paralogs and unprocessed pseudogenes.</P>
+<P>
+In the "pack" and "full" display
+modes, the individual feature names indicate the chromosome, strand, and
+location (in thousands) of the match for each matching alignment.</P>
+
+<H3>Net Track</H3>
+<P>
+The net track shows the best human/$organism chain for
+every part of the $organism genome. It is useful for
+finding orthologous regions and for studying genome
+rearrangement. The human sequence used in this annotation is from
+the Feb. 2009 (hg19) assembly.</P>
+
+<H2>Display Conventions and Configuration</H2>
+<H3>Chain Track</H3>
+<P>By default, the chains to chromosome-based assemblies are colored
+based on which chromosome they map to in the aligning organism. To turn
+off the coloring, check the "off" button next to: Color
+track based on chromosome.</P>
+<P>
+To display only the chains of one chromosome in the aligning
+organism, enter the name of that chromosome (e.g. chr4) in box next to:
+Filter by chromosome.</P>
+
+<H3>Net Track</H3>
+<P>
+In full display mode, the top-level (level 1)
+chains are the largest, highest-scoring chains that
+span this region. In many cases gaps exist in the
+top-level chain. When possible, these are filled in by
+other chains that are displayed at level 2. The gaps in
+level 2 chains may be filled by level 3 chains and so
+forth. </P>
+<P>
+In the graphical display, the boxes represent ungapped
+alignments; the lines represent gaps. Click
+on a box to view detailed information about the chain
+as a whole; click on a line to display information
+about the gap. The detailed information is useful in determining
+the cause of the gap or, for lower level chains, the genomic
+rearrangement. </P>
+<P>
+Individual items in the display are categorized as one of four types
+(other than gap):</P>
+<P><UL>
+<LI><B>Top</B> - the best, longest match. Displayed on level 1.
+<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above
+it.
+<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in
+the opposite orientation.
+<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the
+level above.
+</UL></P>
+
+<H2>Methods</H2>
+<H3>Chain track</H3>
+<P>
+Transposons that have been inserted since the human/$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 human 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>
+
+<H3>Net track</H3>
+<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>
+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 and nets were created
+by Robert Baertsch and Jim Kent.</P>
+<P>
+The chainNet, netSyntenic, and netClass programs were
+developed at the University of California
+Santa Cruz by Jim Kent.</P>
+<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>