6827eaab28004c74be351b4bcb4316264dc42b89 galt Wed Jun 12 01:41:12 2019 -0700 Small html errors found by htmlCheck diff --git src/hg/makeDb/trackDb/drosophila/chainDm2.html src/hg/makeDb/trackDb/drosophila/chainDm2.html index 29893ee..4c6057f 100644 --- src/hg/makeDb/trackDb/drosophila/chainDm2.html +++ src/hg/makeDb/trackDb/drosophila/chainDm2.html @@ -1,100 +1,100 @@ <H2>Description</H2> <P> This track shows <em>$o_organism</em>/<em>$organism</em> genomic alignments using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both <em>$o_organism</em> and <em>$organism</em> simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The <em>$o_organism</em> sequence is from the $o_date ($o_db) assembly.</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 <em>$o_organism</em> assembly or an insertion in the <em>$organism</em> 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 there are multiple chains over a particular portion of the <em>$organism</em> genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.</P> <H2>Display Conventions and Configuration</H2> <P>By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.</P> <P> To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.</P> <H2>Methods</H2> <P> Transposons that have been inserted since the <em>$o_organism</em>/<em>$organism</em> split were removed, and the resulting abbreviated genomes were aligned with blastz. The transposons were then put back into the alignments. The resulting alignments were converted into axt format and the resulting axts fed into axtChain. AxtChain organizes all the alignments between a single <em>$o_organism</em> and a single <em>$organism</em> chromosome into a group and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. Next, maximally scoring chains of these blocks were found by running a dynamic program over the kd-tree. Chains scoring below a threshold were discarded; the remaining chains are displayed here.</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 program <A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>.</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://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf" TARGET=_blank>Scoring pairwise genomic sequence alignments</A>. <em>Pac Symp Biocomput</em>. 2002:115-26. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a> </p> <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 USA</em> <B>100</B>(20), 11484-11489 (2003).</PNatl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9. +<em>Proc Natl Acad Sci USA</em> <B>100</B>(20), 11484-11489 (2003).</P>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 R, 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>