add section on sequence and annotation file formats

docs/file_menu.sgml

@@ -25,74 +25,10 @@ LINKEND="CONCEPTS-ACTIVEENTRY">) and will be the new default entry (see <XREF
 LINKEND="CONCEPTS-DEFAULTENTRY">).
     </PARA>
     <PARA>
+See <XREF LINKEND="FILETYPES">.
 This function only reads the feature section of the input file - the sequence
 (if any) is ignored.
     </PARA>
-    <PARA>
-&prog; can read these feature file formats:
-    </PARA>
-    <ITEMIZEDLIST>
-      <LISTITEM>
-        <PARA>
-          <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/">EMBL or GenBank feature tables</ULINK>
-        </PARA>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-          <ULINK URL="http://www.sequenceontology.org/gff3.shtml">GFF Version 3 files</ULINK>
-        </PARA>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-          FASTA files 
-        </PARA>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-	  Indexed FASTA files can be read in. The files are indexed
-using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK>:
-        </PARA>
-       <SYNOPSIS>
-samtools faidx ref.fasta
-        </SYNOPSIS>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-The indexed FASTA can be used with an indexed GFF to overlay annotation on the sequence. 
-To index the GFF first sort and bgzip the file and then use tabix with "-p gff" option (see the 
-<ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK>):
-        </PARA>
-       <SYNOPSIS>
-(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; 
-tabix -p gff sorted.gff.gz
-        </SYNOPSIS>
-        <PARA>
-A drop down menu of the contigs or chromosomes sequences is provided in the Entry toolbar
-to select the sequence. Using indexed FASTA and indexed GFF files improves the memory management 
-and enables large genomes to be viewed. Note that as it is indexed the sequence and annotation are 
-read-only and cannot be edited. When there are many contigs to select from it can be easier
-to display the one of interest by typing the name into the drop down list.
-        </PARA>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-The output of <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>
-      </LISTITEM>
-      <LISTITEM>
-        <PARA>
-The output of <ULINK URL="http://www.ncbi.nlm.nih.gov/blast/">blastall version
-2.2.2</ULINK> or better.  <COMMAND>blastall</COMMAND> must be run with the
-<COMMAND>-m 8</COMMAND> flag which generates one line of information per HSP.
-Note that currently &prog; displays each Blast HSP as a separate feature
-rather than displaying each BLAST hit as a feature.
-        </PARA>
-      </LISTITEM>
-    </ITEMIZEDLIST>
-  </SECT2>
 
   <SECT2 ID="FILEMENU-READ-ENTRY-INTO">
     <TITLE>Read Entry Into</TITLE>