bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/gbdDescriptionsOld.html src/hg/htdocs/goldenPath/gbdDescriptionsOld.html index 5fb87309662..b5e84c93d48 100755 --- src/hg/htdocs/goldenPath/gbdDescriptionsOld.html +++ src/hg/htdocs/goldenPath/gbdDescriptionsOld.html @@ -25,31 +25,31 @@ <TR><TD WIDTH=10></TD> <TD> <p> <h1><em>This page is retired, you should not use this page. <a href="gbdDescriptions.html"> Please see these instructions about how to use the Table Browser to extract schema information</em></a>.</h1> </p> <P> This page describes the format of the genome annotation databases that underlie the UCSC Genome Browser. These data were contributed by many researchers, as described on the Genome Browser <A HREF="credits.html">Credits</A> page. Please acknowledge the contributor(s) of the data you use. All tables for an assembly are freely usable for any purpose except as indicated in the README.txt file in the downloadable - <A HREF="http://hgdownload.soe.ucsc.edu/downloads.html">annotation + <A HREF="http://hgdownload.gi.ucsc.edu/downloads.html">annotation database directory</A> for that release. </P> <P> </TD><TD WIDTH=15></TD> </TR> </TABLE> <BR> </TD></TR> </TABLE> <BR> <!--Table Descriptions---------------------------------------------------> <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDERCOLOR="888888" BORDER=1> <TR><TD> <TABLE BGCOLOR="D9E4F8" BACKGROUND="../images/hr.gif" WIDTH=100%> @@ -1599,105 +1599,105 @@ - Synteny between mouse and human chromosomes (Last used Apr. 2001) </LI> <LI><A href="#MouseSynWhd">mouseSynWhd</A> - Whitehead synteny between mouse and human chromosomes </LI> <LI><A href="#OrientInfo">mrnaOrientInfo</A> - Extra information on mRNAs calcluated by polyInfo program <LI><A href="#MrnaRefSeq">mrnaRefseq</A> - Associates mRNA IDs with RefSeq IDs <LI><A href="#ScoredRef">multiz5way</A> - Index of multiz multiple alignments of 5 organisms. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#ScoredRef">multiz8way</A> - Index of multiz multiple alignments of 8 organisms. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#WiggleTrack2">multiz8wayCons</A> - "Wiggle track" display of evolutionary conservation in 8 organisms based on a phylogenetic hidden Markov model, using multiz alignments. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#ScoredRef">mzPt1Mm3Rn3Gg2_pHMM</A> - Index of multiz multiple alignments of human, chimp, mouse, rat and chicken. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#WiggleTrack2">mzPt1Mm3Rn3Gg2_pHMM_wig</A> - "Wiggle track" display of evolutionary conservation in human, chimp, mouse, rat, and chicken based on a phylogenetic hidden Markov model, using multiz alignments. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#ScoredRef">multizHg15Mm3</A> - <em>Multiz</em> multiple alignments between human (hg15) and mouse (mm3) </LI> <LI><A href="#ScoredRef">multizMm3Rn2</A> - <em>Multiz</em> multiple alignments between mouse (mm3) and rat (rn2) </LI> <LI><A href="#ScoredRef">multizYeast</A> - <em>Multiz</em> multiple alignments of 7 yeast species against S. cerevisiae (sc1) </LI> <LI><A href="#ScoredRef">mzDy1Dp2Ag1_phast</A> - Index of multiz multiple alignments of <em>D. melanogaster</em>, <em>D. pseudoobscura</em>, and <em>A. gambiae</em> NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#WiggleTrack2">mzDy1Dp2Ag1_phast_wig</A> - "Wiggle track" display of evolutionary conservation in <em>D. melanogaster</em>, <em>D. pseudoobscura</em>, and <em>A. gambiae</em> based on a phylogenetic hidden Markov model, using multiz alignments. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#ScoredRef">mzHg17Mm5_phast</A> - Evolutionary conservation in current species, human, and mouse based on a phylogenetic hidden Markov model, using multiz alignments. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <LI><A href="#WiggleTrack2">mzPt1Mm3Rn3Gg2_pHMM_wig</A> - "Wiggle track" display of evolutionary conservation in current species, human, and mouse based on a phylogenetic hidden Markov model, using multiz alignments. NOTE: To obtain the conservation scores associated with this assembly, download the data from the assembly's <em>phastCons</em> directory - on the Genome Browser <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/" + on the Genome Browser <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/" TARGET=_blank>FTP server</A>. <A NAME="N_GBD"></A> <LI><A href="#BED">nci60</A> - Microarray Experiments for NCI 60 Cell Lines </LI> <LI><A href="#ExpRecord">nci60Exps</A> - Experiment descriptive data</LI> <LI><A href="#NetAlign">netAnoGam1</A> - Database representation of a net of alignments with <em>A. gambiae</em> anoGam1 assembly </LI> <LI><A href="#NetAlign">netCanFam1</A>