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+ obj.onclick = function(e) { + var pix = calculateHgTracksWidth(); + e.currentTarget.href += "&pix=" + pix; + } + } +}); +</script> +</TD></TR> +<!--Content Tables-------------------------------------------------------> +<TR><TD COLSPAN=2 CELLPADDING=10> + <table BGCOLOR="fffee8" WIDTH="100%" BORDERCOLOR="888888" BORDER=1><tr><td> + <table BGCOLOR="D9E4F8" BACKGROUND="../../images/hr.gif" WIDTH=100%><tr><td> + <font SIZE="4"><a NAME="TOC"></a><b> Users Guide for STS Maps vs. Genome Sequence Asembly Comparison Plots</font> + </td></tr></table> + +<!--outer table is for border purposes--> <table BGCOLOR="fffee8" +WIDTH="100%" CELLPADDING=0 CELLSPACING=0><th HEIGHT=15></th><tr><td +WIDTH=10></td><td> + + The purpose of the STS Maps vs. Genome Sequence Assembly + scatter plots is to show the correspondence between previously + constructed genome-wide STS maps and the different clones + maps. We show one plot for each chromosome that displays the + STS marker posistions for the Genethon, Marshfield, GeneMap99, + G3, TNG, Whitehead Integrated and Whitehead-YAC maps. The + y-axis of the plots represent positions in the STS maps, while + the x-axis represents positions in the clone maps. The + primary plots are scaled to fit an entire chromosome on one + page. Additional plots are available which show portions of + each chromosome in fixed scale 50mb windows and 10mb + windows.<P></P> + + Each STS marker is represented by a point that is colored and + shape-coded as described in the legend in the upper right + corner. The horizontal position of the point is the location + of the marker on the clone map of the chromosome in + megabases. The vertical position of the point is the distance + of the marker along the chromosome as determined by one of the + seven STS maps. All seven maps are scaled to have comparable + distance ranges to facilitate comparison. Some markers map to + different chromosomes entirely. These are shown at the top of + the display.<P></P> + + As you mouse-over the graph, the contig you are in, as + determined by your horizontal position, is displayed in the + little window at the bottom of the browser. (Position of this + is dependent on the browser and platform being used.) Clicking + on a contig will bring up a corresponding Summary Page which + is part of our <A HREF="http://genome.ucsc.edu/goldenPath/chromReports"> + Chromosome Reports</A> web pages. This Summary Page displays + information about that particular contig with links to more + detailed information.<P></P> + + <B>Caveats:</B> + <UL> + <LI>Due to the resolution, it is hard to pinpoint the clone + contig for some markers. Go to a higher resolution plot if it + appears that the marker you clicked on is not included in the + report you get. + <LI>We use BLAT to place STS markers, but do + not require an exact match of the STS sequence and/or primer + sequences. This will cause some false positive placements, + and some false negatives as well, mainly due to the draft + nature of the sequence. + <LI>We have not yet incorporated LOD + scores for the markers. + <LI>There are limitations of the + accuracy of each of the seven maps, for more details see + "<A HREF="http://www.nature.com/genomics/human/papers/409860a0_fs_1.html">Initial + sequencing and analysis of the human genome</A>," by the + International Human Genome Sequencing Consortium, Nature, + 409:860-921. + </UL> + <hr> + <address><a href="mailto:booch@cse.ucsc.edu">Terry Furey</a></address> + <!-- Created: Fri Aug 3 13:14:49 PDT 2001 --> + <!-- hhmts start --> +Last modified: Fri Mar 22 13:48:36 PST 2002 +<!-- hhmts end --> +</TD></TR></TABLE> + </TD></TR></TABLE> +</TD></TR></TABLE> + +</TD></TR></TABLE> +</BODY></HTML>