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/human/homoSapiensChainNet.html src/hg/makeDb/trackDb/human/homoSapiensChainNet.html index 269c046..6fb28b9 100644 --- src/hg/makeDb/trackDb/human/homoSapiensChainNet.html +++ src/hg/makeDb/trackDb/human/homoSapiensChainNet.html @@ -1,203 +1,203 @@ <H2>Description</H2> <P> This track shows regions of the human genome that are alignable to other Homo sapiens genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown with thin lines like introns. More description on this display can be found below. </P> <P> Other assemblies included in this track: <ul> <li><a href="https://genome.ucsc.edu/h/GCA_009914755.4" target=_blank>GCA_009914755.4_CHM13_T2T_v2.0</a> human CHM13 T2T v2.0</li> <li><a href="https://genome.ucsc.edu/h/GCA_021951015.1" target=_blank>GCA_021951015.1_HG002.mat.cur.20211005</a> human HG002 maternal</li> <li><a href="https://genome.ucsc.edu/h/GCA_021950905.1" target=_blank>GCA_021950905.1_HG002.pat.cur.20211005</a> human HG002 paternal</li> </ul> </P> <H3>Chain Track</H3> <P> The chain track shows alignments of the human genome to other Homo sapiens genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both source and target assemblies 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 query assembly or an insertion in the target assembly. 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 target 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 Homo sapiens chain for every part of this target human genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. </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> The target and query genomes were aligned with lastz. 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 query chromosome and a single target 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. <pre> # A C G T # A 90 -330 -236 -356 # C -330 100 -318 -236 # G -236 -318 100 -330 # T -356 -236 -330 90 </pre> Chains scoring below a minimum score of "5,000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain:<BR> <pre> tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 </pre> </P> <H3>Net track</H3> <P> Chains were derived from lastz 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> Lastz (previously known as 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 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> Harris, R.S. <a href="http://www.bx.psu.edu/~rsharris/lastz/" target=_blank>(2007) Improved pairwise alignment of genomic DNA</a> Ph.D. Thesis, The Pennsylvania State University </p> <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 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 RC, 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>