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>