<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]-->
<style>
<!--
 /* Font Definitions */
 @font-face
        {font-family:"News Gothic";
        panose-1:2 11 5 0 0 0 0 0 0 0;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0cm;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"News Gothic";}
p.MsoHeader, li.MsoHeader, div.MsoHeader
        {margin:0cm;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"News Gothic";}
p.MsoFooter, li.MsoFooter, div.MsoFooter
        {margin:0cm;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"News Gothic";}
a:link, span.MsoHyperlink
        {color:blue;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {color:purple;
        text-decoration:underline;}
span.E-mailStijl20
        {mso-style-type:personal-compose;
        font-family:Arial;
        color:windowtext;}
 /* Page Definitions */
 @page
        {mso-endnote-separator:url("cid:header.htm\@01C6BC88.2F5AC5D0") es;
        mso-endnote-continuation-separator:url("cid:header.htm\@01C6BC88.2F5AC5D0") ecs;}
@page Section1
        {size:595.3pt 841.9pt;
        margin:70.85pt 70.85pt 70.85pt 70.85pt;
        mso-footer:url("cid:header.htm\@01C6BC88.2F5AC5D0") f1;}
div.Section1
        {page:Section1;}
 /* List Definitions */
 @list l0
        {mso-list-id:1507668903;
        mso-list-type:hybrid;
        mso-list-template-ids:149955852 -151362364 68354073 68354075 68354063 68354073 68354075 68354063 68354073 68354075;}
@list l0:level1
        {mso-level-tab-stop:53.25pt;
        mso-level-number-position:left;
        margin-left:53.25pt;
        text-indent:-18.0pt;}
ol
        {margin-bottom:0cm;}
ul
        {margin-bottom:0cm;}
-->
</style>

</head>

<body lang=NL link=blue vlink=purple>

<div class=Section1>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I am looking for a point where to start in “annotating”
our groups of ESTs/genes….<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Briefly;<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>            I
have a DB containing my 13k ESTs. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>            I
clustered/assembled them after cleaning using the Tiger TGICL tools.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>            Now
I have a “unigene list” of contigs and singletons (about 7k
features).<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>            BLAST
made it possible to “annotate” about half of the sequences further
with known (useful) information.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Now I want to do the following (at best using (semi)
automated conditions (web based or linux based tools));<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:53.25pt;text-indent:-18.0pt;mso-list:
l0 level1 lfo1'><![if !supportLists]><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'><span style='mso-list:Ignore'>1.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>      
</span></font></span></span></font><![endif]><font face=Arial><span lang=EN-GB
style='font-family:Arial'>I would like to know how many genes of which
groups/classes are available and which genes of my set belong to it (i.e. Apoptosis,
development, immunology,…….. This is to get an overview of the
genes present and how complete the repertoire is we finally put onto our
microarray.<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:53.25pt;text-indent:-18.0pt;mso-list:
l0 level1 lfo1'><![if !supportLists]><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'><span style='mso-list:Ignore'>2.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>      
</span></font></span></span></font><![endif]><font face=Arial><span lang=EN-GB
style='font-family:Arial'>Are some of these genes normally tissue specific?<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Any help to get me started into the right direction
is appreciated,<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Alex<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face="News Gothic"><span lang=EN-GB
style='font-size:10.0pt'><o:p> </o:p></span></font></p>

</div>

</body>

</html>