act_start_chapter.sgml

<CHAPTER ID="START">
  <TITLE>Starting &prog;</TITLE>

  <SECT1 ID="COMPARISON-RUN">
    <TITLE>Running a Comparison</TITLE>
    <PARA>
Before running &prog; you will need to obtain a comparison file. 
&prog; supports three different comparison file formats:
    </PARA>
    <ITEMIZEDLIST>
      <LISTITEM>
        <FORMALPARA>
          <TITLE>The output of <ULINK
          URL="http://www.ncbi.nlm.nih.gov/BLAST/">BLAST
            </ULINK> version 2.2.2 or better</TITLE>
          <PARA>
The <COMMAND>blastall</COMMAND> command must be run with the <COMMAND>-m
8</COMMAND> flag which generates one line of information per HSP. If 
<ULINK URL="http://blast.ncbi.nlm.nih.gov/">BLAST+</ULINK>
is used then the legacy_blast.pl PERL script (bundled along with the BLAST+ applications)
can be used to generate the tabular format or run it with the <COMMAND>-outfmt 6</COMMAND> flag.
For more details see the <ULINK URL=
"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/user_manual.pdf">BLAST+ manual</ULINK>.
          </PARA>
        </FORMALPARA>
      </LISTITEM>
      <LISTITEM>
        <FORMALPARA>
          <TITLE>MEGABLAST output</TITLE>
          <PARA>
ACT can also read the output of <ULINK
URL="http://www.ncbi.nlm.nih.gov/blast/megablast.shtml">MEGABLAST</ULINK>,
which is part of the blast distribution.
          </PARA>
        </FORMALPARA>
      </LISTITEM>
      <LISTITEM>
        <FORMALPARA>
          <TITLE>MSPcrunch output</TITLE>
          <PARA>
<ULINK URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"
TYPE="external">MSPcrunch</ULINK> is program for UNIX and GNU/Linux systems
which can post-process <ULINK
URL="http://www.ncbi.nlm.nih.gov/BLAST/">BLAST</ULINK> version 1 output into
an easier to read format.  MSPcrunch much be run with the
<LITERAL>-d</LITERAL> flag.
          </PARA>
        </FORMALPARA>
      </LISTITEM>
    </ITEMIZEDLIST>

    <PARA>
       Anthony Underwood and Jonathan Green at the <ULINK URL="http://www.hpa.org.uk/">
       Health Protection Agency</ULINK> have developed an online tool, <ULINK 
       URL="http://www.hpa-bioinfotools.org.uk/pise/double_act.html">Double ACT</ULINK>, to generate
       ACT comparison files.
    </PARA>

    <PARA>
       Also there is <ULINK URL="http://www.webact.org/">WebACT</ULINK> which was 
       designed and built by James Abbott and David Aanensen at Imperial College, London 
       and is hosted in the laboratory of Professor Brian Spratt at Imperial College London 
       with funding from The Wellcome Trust.
    </PARA>
    
    <SECT2 ID="COMPARISON-BIG-BLAST">
      <TITLE><COMMAND>big_blast.pl</COMMAND></TITLE>
      <PARA>
At the Sanger Centre we generally use a perl script called <ULINK
URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl"
TYPE="external"><LITERAL>big_blast.pl</LITERAL></ULINK> to run blast and
generate a file of results in MSPcrunch format.  To run this script you will
need to install a copy of the Pathogen Sequencing Unit <ULINK
URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/zoo_modules.tar.gz"
TYPE="external">internal perl modules</ULINK>.  <ULINK
URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl"
TYPE="external"><LITERAL>big_blast.pl</LITERAL></ULINK> can also be used to
process blast results after the fact with a command line like this:
      </PARA>

      <PARA>
        <COMMAND>
big_blast.pl blast_results.out
        </COMMAND>
      </PARA>
      <PARA>
Note that big_blast.pl has only been tested on UNIX and GNU/Linux machines.
      </PARA>
    </SECT2>

    <SECT2 ID="COMPARISON-FILE-FORMAT">
      <TITLE>The MSPcrunch Comparison File Format</TITLE>
      <PARA>
Here is an example input file file generated by <LITERAL>MSPcrunch
-d</LITERAL>.
        <SYNOPSIS>
1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq
1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq
828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq
773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.seq
        </SYNOPSIS>
      </PARA>
      <PARA>
The columns have the following meanings (in order): score, percent identity,
match start in the query sequence, match end in the query sequence, query
sequence name, subject sequence start, subject sequence end, subject sequence
name.
      </PARA>
      <PARA>
The columns are separated by spaces.
      </PARA>
    </SECT2>
  </SECT1>

  <SECT1 ID="RUNNINGUNIX">
    <TITLE>Running &prog; on UNIX and GNU/Linux Systems</TITLE>
    <PARA>
On Unix and GNU/Linux the easiest way to run the program is to run the script
called <COMMAND>act</COMMAND> in the &prog; installation directory (see <XREF
LINKEND="INSTALLATION">) like this:
    </PARA>

    <PARA>
      <COMMAND>~/act/act</COMMAND>
    </PARA>

    <PARA>
If all goes well you will be presented with a small window with one menu (the
File menu).  See <XREF LINKEND="LAUNCH-WINDOW"> for a description of this
window.
    </PARA>

    <PARA>
Alternatively you start &prog; with the names of two sequence/EMBL/GENBANK
files and a file containing the comparison data eg:
    </PARA>

    <PARA>
      <COMMAND>
~/act/act sequence1 blast_output.crunch sequence2
      </COMMAND>
    </PARA>

    <PARA>
If you have more than two sequences (there is no upper limit) they should be
listed on the command line separated by the corresponding comparison file:
    </PARA>

    <PARA> 
      <COMMAND>
~/act/act sequence1 seq2_v_seq1.crunch sequence2 seq3_v_seq2.crunch sequence3 
      </COMMAND>
    </PARA>

    <PARA>
See <XREF LINKEND="UNIXARGS"> for a list of the other possible command line
arguments.
    </PARA>

    <PARA>
Here is an alternative way to run &prog; if the <COMMAND>act</COMMAND> script
doesn't work for you:
    </PARA>

    <PARA>
      <COMMAND>
cd ~/act
      </COMMAND>
    </PARA>

    <PARA>
      <COMMAND>
 java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain
      </COMMAND>
    </PARA>
  </SECT1>

&unixargs;

  <SECT1 ID="RUNNINGMAC">
    <TITLE>Running &prog; on Macintosh Systems</TITLE>
    <PARA>
On Macintosh machines &prog; can be started by double clicking on the ACT
icon.
    </PARA>
  </SECT1>

  <SECT1 ID="RUNNINGPC">
    <TITLE>Running &prog; on Windows Systems</TITLE>
    <PARA>
On systems with Java 1.5 (or higher) installed &prog; can be
started by double clicking on the act.jar icon.
    </PARA>
  </SECT1>

  <SECT1 ID="LAUNCH-WINDOW">
    <TITLE>The &prog; Launch Window</TITLE>
    <PARA>
This is the first window that opens when you start &prog;.
    </PARA>

    <SECT2 ID="LAUNCH-WINDOW-FILE-MENU">
      <TITLE>The File Menu</TITLE>
      <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-OPEN">
        <TITLE>Open ...</TITLE>
        <PARA>
If you select this menu item a file requester will be displayed which allows
you to open the sequence files and the comparison files.  If the files you
select are read successfully, a new window will open, which shows the
sequences and the comparison.  See <XREF LINKEND="MAINWINDOW-CHAPTER"> to find
out how to use the main window.  The comparison file is described in <XREF
LINKEND="COMPARISON-FILE-FORMAT">.
        </PARA>
        <PARA>
The "more files ..." button expands the window so that more sequence and
comparison files can be read.
        </PARA>
      </SECT3>

      <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-QUIT">
        <TITLE>Quit</TITLE>
        <PARA>
This menu item will close all windows and then exit the program
        </PARA>
      </SECT3>
    </SECT2>

&options-menu;
  </SECT1>
</CHAPTER>