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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>EuGene : Plugins</title>
<link rel="SHORTCUT ICON" href="Images/eg.jpg">
<link rel="STYLESHEET" type="text/css" href="Style/eugene.css">
<script language="JavaScript1.2" src="Javascripts/slide.js">
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</script>
</head>
<body leftmargin="0" topmargin="0" marginwidth="0" marginheight="0"
bgcolor="white">
<script language="JavaScript1.2" src="Javascripts/euG_menu.js">
</script>
<script type="text/javascript">InitBulle("black","#FFCC66","orange",1);
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<table height="100%" width="100%" cellspacing="0" cellpadding="0"
border="0" rows="2">
<tbody>
<tr height="140">
<td background="Images/top.jpg" colspan="2" height="140"
valign="top"><br>
</td>
</tr>
<tr>
<td width="145" valign="top" align="left"
background="Images/left.jpg"> <img src="Images/left.jpg"
width="145" height="10">
</td>
<td width="100%" valign="top"> <!-- DEBUT PAGE... -->
<table cellspacing="0" cellpadding="6" border="0">
<tbody>
<tr>
<td> <br>
</td>
</tr>
<tr>
<td valign="top" align="justify"> <img
src="Images/m_plugins_on.jpg">
<br>
<br>
Plugins are small software components that can be dynamically
loaded by EuGène. Although it is completely transparent to
the end-user, every plugin loaded by EuGène must be written in
C++ and be a subclass of the Sensor class (for more details see the
EuGène documentation).<br>
<br>
Plugins are presented in 4 categories:<br>
<img src="Images/puce.jpg" width="10">
<a href="plugins.html#signal_plugins">Signal plugins</a><br>
<img src="Images/puce.jpg" width="10">
<a href="plugins.html#content_plugins">Content plugins</a><br>
<img src="Images/puce.jpg" width="10">
<a href="plugins.html#mixed_signal_content_plugins">Mixed signal/content
plugins</a><br>
<img src="Images/puce.jpg" width="10">
<a href="plugins.html#others_plugins">Others plugins</a><br>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="10" cols="2" width="100%">
<tbody>
<tr>
<td valign="top" width="50%">
<div align="center"> <font color="#06768c"> <a
name="signal_plugins"></a> <b> Signal plugins </b></font>
<table width="80%" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td><img height="1" width="100%" src="Images/spacer.jpg">
</td>
</tr>
</tbody>
</table>
</div>
<br>
<table width="100%" cellpadding="1" cellspacing="1">
<tbody>
<tr>
<td>
<table width="100%" cellpadding="2" cellspacing="1">
<tbody>
<tr align="center" class="fonce">
<td><font color="white" size="-1"> <b>Name</b></font></td>
<td><font color="white" size="-1"> <b>Description</b></font></td>
<td nowrap="nowrap"><font color="white" size="-1"> <b>Information
source</b></font></td>
<td><font color="white" size="-1"> <b>Link</b></font></td>
</tr>
<tr class="A0">
<td><font size="-1">ATGpr (obsolete)</font></td>
<td align="justify"> <font size="-1">Injects possible
translation starts as predicted by the ATGpr program.<br>
The plugin reads the prediction of the programs from
two files whose names are derived from the sequence name
by adding the <i>.atgpr</i> and <i>.atgprR</i> suffix (respectively
prediction for the forward and reverse strand).
</font> </td>
<td><font size="-1">ATGpr</font></td>
<td align="center"> <a
href="http://www.hri.co.jp/atgpr/"> <img width="16"
src="Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">EuStop</font></td>
<td align="justify"> <font size="-1">Predicts translation
stops. It is able to deal with noisy sequences and will
eg. predict a possible stop on <i>TGN</i>. </font> </td>
<td><font size="-1">EuGène dummy stop sensor</font></td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">FrameShift</font></td>
<td align="justify"> <font size="-1">Predicts possible
frameshits (either insertions or deletions) at each position
of the sequence with a uniform cost. </font> </td>
<td><font size="-1">EuGène dummy frameshift sensor</font></td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td><font size="-1">GSplicer</font></td>
<td align="justify"> <font size="-1">Injects possible
splice sites as predicted by the GeneSplicer program.<br>
The plugin reads the prediction of the program from
one file whose name is derived from the sequence name by
adding the <i>.Gsplicer</i> suffix. This file describe the predicted
splice sites for the forward and reverse strand.
</font> </td>
<td><font size="-1">GeneSplicer</font></td>
<td align="center"> <a
href="http://www.tigr.org/tdb/GeneSplicer/gene_spl.html"> <img
width="16" src="Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A0">
<td><font size="-1">NG2</font></td>
<td align="justify"> <font size="-1">Injects possible splice
sites as predicted by the NetGene2 program.<br>
The plugin reads the prediction of the programs from
two files whose names are derived from the sequence name
by adding the <i>.splices</i> and <i>.splicesR</i> suffix (respectively
prediction for the forward and reverse strand).
</font> </td>
<td><font size="-1">NetGene2</font></td>
<td align="center"> <a
href="http://www.cbs.dtu.dk/services/NetGene2/"> <img
width="16" src="Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">NStart</font></td>
<td align="justify"> <font size="-1">Injects possible
translation starts as predicted by NetStart program.<br>
The plugin reads the prediction of the program from two
files whose names are derived from the sequence name by adding
the <i>.starts</i> and <i>.startsR</i> suffix (respectively
prediction for the forward and reverse strand). </font>
</td>
<td><font size="-1">NetStart</font></td>
<td align="center"> <a
href="http://www.cbs.dtu.dk/services/NetStart/"> <img
width="16" src="Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A0">
<td><font size="-1">PatConst</font></td>
<td align="justify"> <font size="-1">Predicts a specific
chosen type of signal at each occurence of a given pattern on the sequence.
</font> </td>
<td><font size="-1">-</font></td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td><font size="-1">PepSignal</font></td>
<td align="justify"> <font size="-1">Uses Predotar to predict
peptide adressing sequences after every occurrence of an ATG an modifies
ATG scoring accordingly.</font><br>
</td>
<td><font size="-1"> </font><font size="-1">Predotar</font><br>
</td>
<td align="center"> <a href="http://www.inra.fr/predotar/">
<img width="16" src="Images/world.jpg"
border="0" alt="Predotar - INRA" height="16">
</a>
</td>
</tr>
<tr class="A0">
<td><font size="-1">SMachine</font></td>
<td align="justify"> <font size="-1"> Injects possible signals
as predicted by Splice Machine program.</font> </td>
<td><font size="-1">SpliceMachine</font></td>
<td align="center"> <a href="http://bioinformatics.psb.ugent.be/webtools/splicemachine/">
<img width="16" src="Images/world.jpg"
border="0" alt="SpliceMachine" height="16">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">SpliceWAM</font></td>
<td align="justify"> <font size="-1">Detects the
splice sites and to give them a score reflecting the context
accordance with given models.<br>
A score is attributed at each potential splice sites
(<i>AG</i> / <i>GT</i>), according to Weight Array Method.
</font> </td>
<td><font size="-1">EuGéne Window Array Model for
splice</font></td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">SPred</font></td>
<td align="justify"> <font size="-1">Injects possible splice
sites as predicted by the SplicePredictor program.<br>
The plugin reads the prediction of the programs from
two files whose names are derived from the sequence name by
adding the <i>.spliceP</i> and <i>.splicePR</i> suffix (respectively
prediction for the forward and reverse strand).
</font> </td>
<td><font size="-1"> SplicePredictor</font></td>
<td align="center"> <a
href="http://bioinformatics.iastate.edu/cgi-bin/sp.cgi"> <img
width="16" src="Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">StartWAM</font></td>
<td align="justify"> <font size="-1">Detects the
translation start codons and to give them a score reflecting
the context accordance with given models.<br>
A score is attributed at each potential start codons
(ATG), according to Weight Array Method (see Zhang and
Marr, <i>Comput Appl Biosci.</i> 1993 Oct;9(5):499-509),
or Weighted Array Matrix models (Salzberg, <i>Comput Appl
Biosci</i> 1997 Aug;13(4):365-76). A WAM describes a
consensus motif of a functional signal, and is composed by one
markovian model per each position of the motif. Here the
motif is defined by the ATG (present in all start codons)
plus the two flanking context (informating for the WAM).
Globally, the score of a motif is function of the emission
probabilities of this motif given a true positive model
and a false positive model. </font> </td>
<td><font size="-1">EuGène Window Array Model for
start</font></td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">Transcript</font></td>
<td align="justify"> <font size="-1">Predicts a possible
transcription start and stop at every position, all with
the same uniform cost. </font> </td>
<td><font size="-1">EuGène dummy transcript start/stop
sensor</font></td>
<td align="center">-</td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
</td>
</tr>
<tr>
<td valign="top" width="50%">
<div align="center"> <font color="#06768c"> <a
name="content_plugins"></a> <b> Content plugins </b></font>
<table width="80%" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td><img height="1" width="100%" src="Images/spacer.jpg">
</td>
</tr>
</tbody>
</table>
</div>
<br>
<table width="100%" cellpadding="2" cellspacing="1">
<tbody>
<tr align="center" class="fonce">
<td><font color="white" size="-1"> <b>Name</b></font></td>
<td><font color="white" size="-1"> <b>Description</b></font></td>
<td><font color="white" size="-1"> <b>Information source</b></font></td>
<td><font color="white" size="-1"> <b>Link</b></font></td>
</tr>
<tr class="A0">
<td><font size="-1">BlastX</font></td>
<td align="justify"> <font size="-1">Exploit similarities
with homologous proteins.<br>
The similarities influence exon and intron detection.
Similarities from several databases can be exploited.
Usually 3 databases are used: SwissProt, PIR and TrEMBL.
</font> </td>
<td><font size="-1">BlastX-based proteic similarity sensor</font></td>
<td align="center"> <a
href="http://www.ncbi.nlm.nih.gov/BLAST/"> <img width="16"
src="file:///home/cros/Linux/EuGeneWEB/Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">Est</font></td>
<td align="justify"> <font size="-1">Take into account
information from aligned transcribed sequences, both complete
cDNA and EST.<br>
The existence of a hit (resp. gap) in the spliced alignment
will influence intergenic, exonic and intronic state costs
by penalizing states that are incompatible with the alignment. The
spliced alginments must be performed beforehand using
a spliced aligner such as <i>sim4</i> or <i>spidey</i>.
The output of these aligners must be converted in the adequate
format. </font> </td>
<td><font size="-1">Sim4-based transcription similarity
sensor</font></td>
<td align="center"> <a
href="http://pbil.univ-lyon1.fr/sim4.php"> <img width="16"
src="file:///home/cros/Linux/EuGeneWEB/Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A0">
<td><font size="-1">Homology</font></td>
<td align="justify"> <font size="-1">Exploit exon conservation.
</font> </td>
<td><font size="-1">TBlastX-based exon conservation sensor</font></td>
<td align="center"> <a
href="http://www.ncbi.nlm.nih.gov/BLAST/"> <img width="16"
src="file:///home/cros/Linux/EuGeneWEB/Images/world.jpg" border="0">
</a></td>
</tr>
<tr class="A1">
<td><font size="-1">MarkovConst</font></td>
<td align="justify"> <font size="-1">A simulated contents
sensor that gives constant probabilities to all positions
for each region type.<br>
Two parameters (in the EuGène parameters file)
indicate the GC scope of the contents sensor. If the GC% of
the sequence is out of the scope, the plugin will give an equal
null loglikelihood to all types of regions. Used for
testing purposes and for simulating the exponential length
distributions of HMM. </font> </td>
<td><font size="-1">EuGène dummy constant probabilities</font></td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">MarkovIMM</font></td>
<td align="justify"> <font size="-1">Injects coding/intronic/utr/intergenic
likelihood as modeled by interpolated Markov models
(introduced in Glimmer).<br>
These models are defined in a so-called matrices file.
Depending on the matrices file, this may contain IMM for exons,
introns and intergenic data and also optionnally 5' and
3' UTR regions. If these 2 last IMMs are absent from the matrices
file, intronic models are used for UTR. </font> </td>
<td><font size="-1">EuGène DNA level interpolated
markov models</font></td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td><font size="-1">MarkovProt</font></td>
<td align="justify"> <font size="-1">Injects coding/non
coding likelihood as modeled by proteic Markov models.<br>
These models are defined in a matrices file. The order
of the Markov model must be given in the EuGène parameters
file. </font> </td>
<td><font size="-1">EuGène amino acid level markov
models</font></td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">Repeat</font></td>
<td align="justify"> <font size="-1">Exploit the output of
repeated sequences detector such as RepeatMasker by penalizing
exonic, inronic or UTR states when repeats are detected.
</font> </td>
<td><font size="-1">RepeatMasker</font></td>
<td align="center"> <a
href="http://ftp.genome.washington.edu/cgi-bin/RepeatMasker">
<img width="16" src="Images/world.jpg" border="0">
</a></td>
</tr>
</tbody>
</table>
</td>
</tr>
<tr>
<td valign="top" width="50%">
<div align="center"> <font color="#06768c">
<a name="mixed_signal_content_plugins"></a> <b> Mixed Signal/Content
plugins </b></font>
<table width="80%" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td><img height="1" width="100%" src="Images/spacer.jpg">
</td>
</tr>
</tbody>
</table>
</div>
<br>
<table width="100%" cellpadding="1" cellspacing="1">
<tbody>
<tr>
<td>
<table width="100%" cellpadding="2" cellspacing="1">
<tbody>
<tr align="center" class="fonce">
<td><font color="white" size="-1"> <b>Name</b></font></td>
<td><font color="white" size="-1"> <b>Description</b></font></td>
<td nowrap="nowrap"><font color="white" size="-1"> <b>Information
source</b></font></td>
<td><font color="white" size="-1"> <b>Link</b></font></td>
</tr>
<tr class="A0">
<td><font size="-1">AnnotaStruct</font></td>
<td align="justify"> <font
size="-1">Take into account arbitrary user information using GFF files.
High level information of either CDS or transcript elements can be given
as well as low-level information on signals or regions.</font><br>
</td>
<td><font size="-1">GFF file</font><br>
</td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td> <font size="-1">IfElse</font> </td>
<td align="justify"> <font size="-1">Combine the predictions
of two existing plugins.<br>
It listen to a first plugin. For each possible predictable
item, if this plugin predicts something then this prediction
is used. If the plugin does not predict anything, then the output
of the second plugin is used. </font> </td>
<td> <font size="-1">EuGène information combination</font>
</td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td><font size="-1">Riken</font></td>
<td align="justify"> <font size="-1">Full-length mRNA.<br>
A file with extension <i>.riken</i> is read. Each line
must contain the positions of the extremities of the match
of the 5' EST then the name of the 5' EST the same thing for the
3'EST then the name of the clone. </font> </td>
<td><font size="-1">Full-length mRNA </font></td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td> <font size="-1">User (obsolete)</font> </td>
<td align="justify"> <font size="-1">Take into account
specific user information (usefull to explore alternative
gene structures).<br>
A <font color="#ad3000"
onmouseover="AffBulle('<table width=100% border=0 CELLSPACING=1 CELLPADDING=1><tr bgcolor=orange><td colspan=4 align=center><font face=arial size=-1><b>USER information </b><i>(click for details)</font></td></tr></table><table align=center width=100% border=0 CELLSPACING=0 CELLPADDING=0><tr bgcolor=orange><td><table border=0 CELLSPACING=1 CELLPADDING=0><tr bgcolor=#FFCC66><td colspan=4><font face=arial size=-1>The prediction can take into account specific user information (usefull to explore<br>alternative gene structures). A simple language is required :</font></td></tr><tr bgcolor=#FFCC66><td colspan=2 align=center><font face=arial size=-1><b>Signals</b></font></td><td colspan=2 align=center><font face=arial size=-1><b>Sequence itself</b></font></td></tr><tr bgcolor=#FFCC66><td><font face=arial size=-1><i> type </i></font></td><td><font face=arial size=-1> start stop acceptor donor </font></td><td><font face=arial size=-1><i> type </i></font></td><td><font face=arial size=-1> exon intron utr5/3 intergenic </font></td></tr><tr bgcolor=#FFCC66><td><font face=arial size=-1><i> strand </i></font></td><td><font face=arial size=-1> f = forward / r = reverse </font></td><td><font face=arial size=-1><i> strand </i></font></td><td><font face=arial size=-1> f = forward / r = reverse </font></td></tr><tr bgcolor=#FFCC66><td colspan=2></td><td><font face=arial size=-1><i> frame </i></font></td><td><font face=arial size=-1> only for exons / introns </font></td></tr><tr bgcolor=#FFCC66><td><font face=arial size=-1><i> position </i></font></td><td><font face=arial size=-1> position on the sequence </font></td><td><font face=arial size=-1><i> [start..end] </i></font></td><td><font face=arial size=-1> scope of the information </font></td></tr><tr bgcolor=#FFCC66><td><font face=arial size=-1><i> value </i></font></td><td><font face=arial size=-1> float between 0.0, 1.0</font></td><td><font face=arial size=-1><i> value </i></font></td><td><font face=arial size=-1> float between -infinity, infinity </font></td></tr></table></td></tr></table>')"
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<b><u>simple language</u></b></font> is required containing
statements on signals and on the sequence itself. </font>
</td>
<td> <font size="-1">EuGène arbitrary user information
sensor (language based)</font> </td>
<td align="center">-</td>
</tr>
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<td valign="top" width="50%">
<div align="center"> <font color="#06768c"> <a
name="others_plugins"></a> <b> Others plugins </b></font>
<table width="80%" cellpadding="0" cellspacing="0">
<tbody>
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<td><img height="1" width="100%" src="Images/spacer.jpg">
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<br>
<table width="100%" cellpadding="2" cellspacing="1">
<tbody>
<tr align="center" class="fonce">
<td><font color="white" size="-1"> <b>Name</b></font></td>
<td><font color="white" size="-1"> <b>Description</b></font></td>
<td><font color="white" size="-1"> <b>Information source</b></font></td>
<td><font color="white" size="-1"> <b>Link</b></font></td>
</tr>
<tr class="A0">
<td> <font size="-1">GCPlot</font> </td>
<td align="justify"> <font size="-1">Add to the graphical
representation a plot of basic composition statistics
on the sequence.<br>
The composition statistics represented can be arbitrarily
chosen. For example, the <i>GC%=(G+C)/(A+T+G+C)</i>
Statistics on the 3rd base of each codon are automatically
computed and plotted. The color (integer between 0 and
8), the smoothing window width and a zooming factor can be specified.
The zooming factor for the 3rd base in each codon in
zoomed using specific zooming factor. </font> </td>
<td> <font size="-1">EuGène basic composition statitics
plot</font> </td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td> <font size="-1">GFF</font></td>
<td align="justify"> <font size="-1">Add to the graphical
representation an annotation provided in a GFF format.<br>
Note that the provided GFF annotation could be an EuGène
prediction given in GFF format (obtained using the <i>-pg</i>
argument). This could allow to visualise two predictions on the
same graph. For a sequence, the plugin reads the annotation
from one file whose name is derived from the sequence
name by adding the <i>.gff</i> suffix. </font> </td>
<td> <font size="-1">EuGène gff annotation plot</font>
</td>
<td align="center">-</td>
</tr>
<tr class="A0">
<td> <font size="-1">Plotter</font> </td>
<td align="justify"> <font size="-1">Add to the graphical
representation the GC%, the GC3% and the two quotients
A/T+A and T/T+A. </font> </td>
<td> <font size="-1">EuGène GC%, GC3%, A/AT% T/AT%
plot</font> </td>
<td align="center">-</td>
</tr>
<tr class="A1">
<td> <font size="-1">Tester</font> </td>
<td align="justify"> <font size="-1">Evaluate signal sensors.
<br>
For a sequence, the plugin reads the truth gene coordinates from
one file whose name is derived from the sequence name
by adding the <i>.gff</i> suffix, and creates one file
<i>test.sensorName.gff</i> for each sensor tested.
</font> </td>
<td> <font size="-1">EuGène signal sensors test</font>
</td>
<td align="center">-</td>
</tr>
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