bbabbd5d2566d47d923d51dbe350634783455999
mspeir
  Sun Oct 26 12:14:52 2025 -0700
change soe to gi, refs #35031

diff --git src/hg/htdocs/goldenPath/help/hgTablesHelp.html src/hg/htdocs/goldenPath/help/hgTablesHelp.html
index e3ed79e3c2b..c9297430b0d 100755
--- src/hg/htdocs/goldenPath/help/hgTablesHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTablesHelp.html
@@ -102,31 +102,31 @@
   display basic statistics calculated over a selected data set</li> 
   <li> 
   display the schema for table and list all other tables in the database connected to the table</li>
   <li> 
   organize the output data into several different formats for use in other applications, 
   spreadsheets, or databases</li> 
 </ul> 
 <p> 
 This User's Guide is aimed at both the novice Table Browser user as well the advanced user. If you 
 are new to the Table Browser, read the <a href="#GettingStarted">Getting started</a> section to 
 learn about browser basics and try some simple queries. Advanced users may want to proceed directly 
 to the section that addresses a particular area of functionality in detail.</p> 
 <p> 
 Although the Table Browser provides sufficient flexibility to satisfy the needs of most users, some 
 advanced users may require the ability to run SQL commands directly on the Genome Browser database.
-UCSC provides two public MariaDB servers: (1) genome-mysql.soe.ucsc.edu (US West Coast),
+UCSC provides two public MariaDB servers: (1) genome-mysql.gi.ucsc.edu (US West Coast),
 (2) genome-euro-mysql.soe.ucsc.edu (Europe). More information can be found on our
 <a href="mysql.html">MariaDB Access</a> page. Alternatively, the database may be
 downloaded to a local computer for MariaDB access. See the <a href="mirror.html">mirror 
 site</a> documentation for information on setting up a local copy of the database.</p>
 
 <!-- ====Tables======================== -->
 <a name="Tables"></a>
 <h2>About the Table Browser databases and tables</h2> 
 <p> 
 The Table Browser is built on top of the Genome Browser database</a>, which actually consists of 
 several separate databases, one for each genome assembly.</p>  
 <p> 
 Tables within the databases may be differentiated by whether the data are based on genome start-stop
 coordinates (positional tables) or are independent of position (non-positional tables).Some output 
 formats and query options are applicable only to positional tables, hence the distinction.</p> 
@@ -769,31 +769,31 @@
 <h3>Displaying CDS FASTA alignments</strong> (genePred tables only)</h3>
 <p> 
 The CDS FASTA alignments are created from a Multiple Alignment File 
 (<a href="../../FAQ/FAQformat.html#format5">MAF</a>) in combination with a 
 <a href="../../FAQ/FAQformat.html#format9">genePred</a> table. The UCSC MAF format stores multiple 
 alignments at the DNA level between entire genomes. You can use the Table Browser to return FASTA 
 alignments of coding regions in nucleotide-space or translated into amino acid-space. However, it is
 worth noting that the initial MAF files are all created by aligning genomes at the DNA level.</p> 
 <p> 
 <strong>Genome-wide CDS FASTA alignments</strong><br> 
 Note that when using the Table Browser to fetch CDS FASTA output, it is best to restrict your query 
 to a reasonable-sized position range rather than requesting output from the entire genome. A 
 genome-wide query will take a substantial amount of compute time, and it is likely that your 
 Internet browser will time out and disconnect. If you would like to download genome-wide CDS FASTA 
 output for any of several model organisms, you can do so from the 
-<a href="http://hgdownload.soe.ucsc.edu">download server</a>.</p> 
+<a href="http://hgdownload.gi.ucsc.edu">download server</a>.</p> 
 <p> 
 <strong>Creating CDS FASTA alignments using the Table Browser</strong><br> 
 To display FASTA multiple alignments for the CDS regions of genes, select the <em>CDS FASTA 
 alignment from multiple alignment</em> option in the <code>output format</code> list. In order to 
 see this output format option, you must have a genePred table selected. If you limit your search to 
 a certain position range within the genome (rather than searching the entire genome), the tool will 
 return FASTA alignments for all genes that overlap the position for which you are searching. The 
 Table Browser will present you with a configuration page. On this page, you can select options for 
 your output.</p> 
 <p> 
 First, select your MAF table.  This is the table from which the multiple alignments will be 
 extracted for the CDS regions of your gene track. If you do not know the name of the MAF table that 
 corresponds to the Conservation track, you can find it in the Genome Browser by following these 
 <a href="../../FAQ/FAQtracks.html#tracks21">instructions</a>.</P> 
 <p>