7149c3be130a904c8bae3802b15cda69833c52a0
lrnassar
  Mon Mar 18 17:00:30 2024 -0700
Adding some info to hgPcr to be wary of primer identification using only this tool. We have had users who used hgPcr, ordered primers, and then found they had off-targets. Refs #25202

diff --git src/hg/hgPcr/hgPcr.c src/hg/hgPcr/hgPcr.c
index 2bfd5b3..1fae732 100644
--- src/hg/hgPcr/hgPcr.c
+++ src/hg/hgPcr/hgPcr.c
@@ -207,30 +207,35 @@
 hFreeConn(&conn2);
 slReverse(&serverList);
 return serverList;
 }
 
 void doHelp()
 /* Print up help page */
 {
 puts(
 "In-Silico PCR searches a sequence database with a pair of\n"
 "PCR primers, using an indexing strategy for fast performance.\n"
 "See an example\n"
 "<a href='https://youtu.be/U8_QYwmdGYU'"
 "target='_blank'>video</a>\n"
 "on our YouTube channel.\n"
+"This tool is not guaranteed to find off-target locations for\n"
+"primers, it is optimized for 100% identical matches. For\n"
+"use in primer design consider additional validation with tools such as\n"
+"<a target='_blank' href='https://www.ncbi.nlm.nih.gov/tools/primer-blast/'>"
+"primer blast</a>.\n"
 "\n"
 "<H3>Configuration Options</H3>\n"
 "<B>Genome and Assembly</B> - The sequence database to search.<BR>\n"
 "<B>Target</B> - If available, choose to query transcribed sequences.<BR>\n" 
 "<B>Forward Primer</B> - Must be at least 15 bases in length.<BR>\n"
 "<B>Reverse Primer</B> - On the opposite strand from the forward primer. Minimum length of 15 bases.<BR>\n"
 "<B>Max Product Size</B> - Maximum size of amplified region.<BR>\n"
 "<B>Min Perfect Match</B> - Number of bases that match exactly on 3' end of primers.  Minimum match size is 15.<BR>\n"
 "<B>Min Good Match</B> - Number of bases on 3' end of primers where at least 2 out of 3 bases match.<BR>\n"
 "<B>Flip Reverse Primer</B> - Invert the sequence order of the reverse primer and complement it.<BR>\n"
 "<B>Append to existing PCR result</B> - Add this PCR result list to the currently existing track of PCR results.<BR>\n"
 "\n"
 "<H3>Output</H3>\n"
 "When successful, the search returns a sequence output file in fasta format \n"
 "containing all sequence in the database that lie between and include the \n"