From 4987786077a4f32d0d4c7571c7ced7b464275f3f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 5 Jan 2011 12:50:31 +0000
Subject: [PATCH] update
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15310 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
docs/file_menu.sgml | 15 ++++++++++++---
1 file changed, 12 insertions(+), 3 deletions(-)
diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index b5b66a3ed..3e2b8c0c7 100644
--- a/docs/file_menu.sgml
+++ b/docs/file_menu.sgml
@@ -34,18 +34,27 @@ This function only reads the feature section of the input file - the sequence
<ITEMIZEDLIST>
<LISTITEM>
<PARA>
- <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html">EMBL or GenBank feature tables</ULINK>
+ <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/">EMBL or GenBank feature tables</ULINK>
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
- <ULINK URL="http://song.sourceforge.net/gff3.shtml">GFF Version 3 files</ULINK>
+ <ULINK URL="http://www.sequenceontology.org/gff3.shtml">GFF Version 3 files</ULINK>
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+ FASTA files and in addition indexed FASTA files can be used. The files are indexed
+using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK> (e.g.
+<COMMAND>samtools faidx ref.fasta</COMMAND>). A drop down menu of the contigs or chromosomes
+is provided in the Entry toolbar to select the sequence. Using indexed FASTA files
+improves the memory management and enables large genomes to be viewed.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The output of <ULINK
-URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"><COMMAND>MSPcrunch</COMMAND></ULINK>.
+URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"><COMMAND>MSPcrunch</COMMAND></ULINK>.
<COMMAND>MSPcrunch</COMMAND> must be run with the <COMMAND>-x</COMMAND> or
<COMMAND>-d</COMMAND> flags.
</PARA>
--
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