04485bb7385b73d2ce5187ac6b4a8633a651b00c
galt
  Thu Jan 10 14:16:22 2013 -0800
fixing blat documentation to match our use of stepSize=5 with hgBlat/gfServer which we have been doing since hgPcr came out.
diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 6ccca13..b2a53f5 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -708,82 +708,64 @@
 "submissions is 50,000 bases or 25,000 letters.\n</P>");
 if (hgPcrOk(db))
     printf("<P>For locating PCR primers, use <A HREF=\"../cgi-bin/hgPcr?db=%s\">In-Silico PCR</A>"
            " for best results instead of BLAT.</P>", db);
 puts("</TD></TR></TABLE>\n");
 
 
 
 printf("</FORM>\n");
 
 webNewSection("About BLAT");
 printf( 
 "<P>BLAT on DNA is designed to\n"
 "quickly find sequences of 95%% and greater similarity of length 25 bases or\n"
 "more.  It may miss more divergent or shorter sequence alignments.  It will find\n"
-"perfect sequence matches of 25 bases, and sometimes find them down to %d bases.\n"
+"perfect sequence matches of 20 bases.\n"
 "BLAT on proteins finds sequences of 80%% and greater similarity of length 20 amino\n"
 "acids or more.  In practice DNA BLAT works well on primates, and protein\n"
-"blat on land vertebrates.",
-   minMatchShown
+"blat on land vertebrates."
 );
-if (hIsGsidServer())
-{
-printf("%s",
-"\n</P><P>BLAT is not BLAST.  DNA BLAT works by keeping an index of the entire genome\n"
-"in memory.  The index consists of all non-overlapping 11-mers except for\n"
-"those heavily involved in repeats.  The index takes up a bit less than\n"
-"a gigabyte of RAM.  The genome itself is not kept in memory, allowing\n"
-"BLAT to deliver high performance on a reasonably priced Linux box.\n"
-"The index is used to find areas of probable homology, which are then\n"
-"loaded into memory for a detailed alignment. Protein BLAT works in a similar\n"
-"manner, except with 4-mers rather than 11-mers.  The protein index takes a little\n"
-"more than 2 gigabytes.</P>\n"
-"<P>BLAT was written by <A HREF=\"mailto:kent@soe.ucsc.edu\">Jim Kent</A>.\n"
-"Sources and executables to run batch jobs on your own server are available free\n"
-"for academic, personal, and non-profit purposes.  Non-exclusive commercial\n"
-"licenses are also available. See the \n"
-"<A HREF=\"http://www.kentinformatics.com\" TARGET=_blank>Kent Informatics</A>\n"
-"website for details.</P>\n"
-"\n"
-"<P>For more information on the graphical version of BLAT, click the Help \n"
-"button on the top menu bar. </P> \n");
-}
-else
-{
+
+
 printf("%s",
 "\n</P><P>BLAT is not BLAST.  DNA BLAT works by keeping an index of the entire genome\n"
-"in memory.  The index consists of all non-overlapping 11-mers except for\n"
-"those heavily involved in repeats.  The index takes up a bit less than\n"
-"a gigabyte of RAM.  The genome itself is not kept in memory, allowing\n"
+"in memory.  The index consists of all overlapping 11-mers stepping by 5 except for\n"
+"those heavily involved in repeats.  The index takes up about\n"
+"2 gigabytes of RAM.  RAM can be further reduced to less than 1 GB by increasing step size to 11.\n"
+"The genome itself is not kept in memory, allowing\n"
 "BLAT to deliver high performance on a reasonably priced Linux box.\n"
 "The index is used to find areas of probable homology, which are then\n"
 "loaded into memory for a detailed alignment. Protein BLAT works in a similar\n"
 "manner, except with 4-mers rather than 11-mers.  The protein index takes a little\n"
 "more than 2 gigabytes.</P>\n"
 "<P>BLAT was written by <A HREF=\"mailto:kent@soe.ucsc.edu\">Jim Kent</A>.\n"
 "Like most of Jim's software, interactive use on this web server is free to all.\n"
 "Sources and executables to run batch jobs on your own server are available free\n"
 "for academic, personal, and non-profit purposes.  Non-exclusive commercial\n"
 "licenses are also available. See the \n"
 "<A HREF=\"http://www.kentinformatics.com\" TARGET=_blank>Kent Informatics</A>\n"
 "website for details.</P>\n"
 "\n"
 "<P>For more information on the graphical version of BLAT, click the Help \n"
-"button on the top menu bar or see the Genome Browser \n"
-"<A HREF=\"../FAQ/FAQblat.html\">FAQ</A>. </P> \n");
-}
+"button on the top menu bar");
+
+if (hIsGsidServer())
+    printf(". </P> \n");
+else
+    printf(" or see the Genome Browser <A HREF=\"../FAQ/FAQblat.html\">FAQ</A>. </P> \n");
+
 }
 
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 char *userSeq;
 char *db, *organism;
 boolean clearUserSeq = cgiBoolean("Clear");
 
 cart = theCart;
 dnaUtilOpen();
 
 getDbAndGenome(cart, &db, &organism, oldVars);
 char *oldDb = cloneString(db);
 findClosestServer(&db, &organism);