[med-svn] r141 - trunk/packages/sigma-align/trunk/debian

[Charles Plessy]

Author: charles-guest
Date: 2006-10-04 14:23:05 +0000 (Wed, 04 Oct 2006)
New Revision: 141

Modified:
   trunk/packages/sigma-align/trunk/debian/changelog
   trunk/packages/sigma-align/trunk/debian/sigma.1.xml
Log:
Enhancing manpage with quotes from the website

Modified: trunk/packages/sigma-align/trunk/debian/changelog
===================================================================
--- trunk/packages/sigma-align/trunk/debian/changelog	2006-09-28 11:57:21 UTC (rev 140)
+++ trunk/packages/sigma-align/trunk/debian/changelog	2006-10-04 14:23:05 UTC (rev 141)
@@ -1,3 +1,9 @@
+sigma-align (1.0-2) unstable; urgency=low
+
+  * Enhancing manpage with quotes from the website. 
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Wed,  4 Oct 2006 23:21:59 +0900
+
 sigma-align (1.0-1) unstable; urgency=low
 
   * Initial release Closes: #378289

Modified: trunk/packages/sigma-align/trunk/debian/sigma.1.xml
===================================================================
--- trunk/packages/sigma-align/trunk/debian/sigma.1.xml	2006-09-28 11:57:21 UTC (rev 140)
+++ trunk/packages/sigma-align/trunk/debian/sigma.1.xml	2006-10-04 14:23:05 UTC (rev 141)
@@ -5,7 +5,7 @@
 
   <!ENTITY dhfirstname "<firstname>Charles</firstname>">
   <!ENTITY dhsurname   "<surname>Plessy</surname>">
-  <!ENTITY dhdate      "<date>september 5, 2006</date>">
+  <!ENTITY dhdate      "<date>October 4 , 2006</date>">
   <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
   <!ENTITY dhemail     "<email>charles-debian-nospam at plessy.org</email>">
   <!ENTITY dhusername  "Charles Plessy">
@@ -135,8 +135,28 @@
       </varlistentry>
     </variablelist>
   </refsect1>
- 
+  
   <refsect1>
+    <title>MORE HELP</title>
+    <para>
+      The "significance" parameter (<option>-x</option>) determines whether local alignments are accepted or rejected. The default at present is 0.002. Experiments on synthetic data (described in the paper) suggest that 0.002 is about the threshold where sigma fails to align phylogenetically-unrelated data that has moderate (yeast-like) dinucleotide correlation.
+    </para>
+    <para>
+      Using a <quote>background model</quote> appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the <option>-b</option> parameter, a FASTA-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence).
+    </para>
+    <para>
+      Instead of this, if the single-site and dinucleotide frequencies are known already, they may be supplied in a file via the -B option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored).
+    </para>
+  </refsect1>
+  
+  <refsect1>
+    <title>AUTHOR</title>
+    <para>
+      &dhpackage; was written by Rahul Siddharthan, The Institute of Mathematical Sciences, Chennai, India. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases.
+    </para>
+  </refsect1>
+  
+  <refsect1>
     <title>REFERENCE</title>
     <para>
       Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly-conserved non-coding DNA sequence BMC Bioinformatics 2006, 7:143     doi:10.1186/1471-2105-7-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471-2105/7/143/</para>