5fc81fc9aeef72ee718678ce93da39337b2db6fe markd Tue Dec 3 19:50:33 2024 -0800 fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references diff --git src/hg/makeDb/trackDb/mouse/altSeqComposite.html src/hg/makeDb/trackDb/mouse/altSeqComposite.html index 0b9610b..e879877 100644 --- src/hg/makeDb/trackDb/mouse/altSeqComposite.html +++ src/hg/makeDb/trackDb/mouse/altSeqComposite.html @@ -1,217 +1,221 @@ <h2>Description</h2> <p> This track shows alternate sequence indicated by the <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml" target="_blank">GRC</a> (Genome Reference Consortium) to the GRCm38 (mm10) reference sequence in an effort to provide the best possible reference assembly for the mouse genome. The GRC does this by both generating multiple representations, alternate loci, for regions that are too complex to be represented by a single path and by releasing regional fixes to short sections of DNA known as patches. This allows users who are interested in a specific locus to get an improved representation without affecting users who need chromosome coordinate stability. </p> <a href="http://hgdownload.soe.ucsc.edu/gbdb/mm10/$o_db/" target="_blank">Download</a> the GRC Patch Release track data sets from the Genome Browser downloads server. <h3><font color="#FF0000">Patches</font></h3> <p> Items in the <em>Patch</em> track indicate areas of the sequence that have been corrected by the GRC and will be updated to new sequence in the next full mouse assembly release. To view the new, corrected sequence, click on the "Fetch alternate sequence" link that appears on the sequence details pages. Data points in this track are always displayed in <font color="#FF0000"><b>red</b></font>. </p> <h3>Alignment</h3> <p> The <em>Alignment</em> track is the PSL representation of the <em>Chain</em> track. This PSL representation allows the side-by-side alignment to be viewed. It was created from the Chain track data using the <em>chainToPsl</em> kent source utility. This track follows the display conventions for <a href="/goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank"> PSL alignment tracks</a>. Alignments are displayed in <b>black</b> and, depending on the track configuration settings, may be interspersed with vertical <font color="#F88017"><b>orange</b></font> lines. </p> <h3>Chain Track</h3> <p> The chain track shows the alignment of mouse genome alternate sequence to the mouse $date genome sequence using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and the alternate sequence simultaneously. </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 mouse assembly or an insertion in the alternate sequence. Double lines represent more complex gaps that involve substantial sequence in both sequences. </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. 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 (click "Chains" text in controls to view options). </p> <p> To display only the chains of one chromosome in the aligning sequence, enter the name of that chromosome (e.g., chr4) in box next to: Filter by chromosome (click "Chains" text in controls to view options). </p> <p> Data points in this track are displayed according to the chromosome color key that appears just below the Browser display (e.g., data points on chromosome 14 appear in <font color="#0000CC"><b>this color</b></font>). </p> <h3>Net Track</h3> <p> The net track shows the best mouse/alternate chain for every part of the alternate sequence. It is useful for finding orthologous regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the $date assembly. </p> <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> <li><b>Syn</b> - Line-ups on the same chromosome as the gap in the level above it.</li> <li><b>Inv</b> - A line-up on the same chromosome as the gap above it, but in the opposite orientation.</li> <li><b>NonSyn</b> - A match to a chromosome different from the gap in the level above.</li> </ul></p> <p> Data points in this track are displayed according to the chromosome color key that appears just below the Browser display (e.g., data points on chromosome 14 appear in <font color="#0000CC"><b>this color</b></font>). </p> <h2>Methods</h2> <h3>Patch Tracks</h3> <p> The locations of the Patches were established by NCBI and specified in the files at:<br> <a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38.p1/PATCHES/alt_scaffolds/" target="_blank">ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38.p1/PATCHES/alt_scaffolds/</a>alt_scaffold_placement.txt </p> <h3>Chain Track</h3> <p> The lastz alignments between the mouse sequence and the alternate sequence were restricted to only the region of the mouse sequence that is replaced by the updated patch sequence. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between the single mouse region of the alignment and a single region from the alternate sequence 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. $matrix </p> <p> Chains scoring below a minimum score of '$chainMinScore' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain:<br> $chainLinearGap </p> <h3>Net Track</h3> <p> Chains were derived from lastz alignments, using the methods described in the chain track description above, 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 sequences 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> +LASTZ was developed at +<A HREF="http://www.bx.psu.edu/~rsharris/lastz/" TARGET=_blank>Miller Lab at Pennsylvania State University</A> by +Bob Harris. +</P> <p> Lineage-specific repeats were identified by Arian Smit and his <a href="https://www.repeatmasker.org/" target="_blank">RepeatMasker</a> program. </p> <p> The axtChain program was developed at the University of California 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> <h2>References</h2> +<P> +Harris RS. +<a href="http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf" +target="_blank">Improved pairwise alignment of genomic DNA</a>. +<em>Ph.D. Thesis</em>. Pennsylvania State University, USA. 2007. +</P> <p> Chiaromonte F, Yap VB, Miller W. <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" 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/content/100/20/11484.abstract" 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://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. </p>