<p>
<font face="Arial,Helvetica"><font color="#330033">Local
search on a specific sequence and database. This program gives you the "<a href="#acce">acceptability</a>"
of the specific organism to a given sequence and</font></font> <font face="Arial,Helvetica"><font color="#330033">reports
HTML outputs. See a example <a href="http://guitar.rockefeller.edu/~marcius/ClonErrNet/xtras/example.html">output</a>
file for a search with the precursor of the envelope polyprotein GP160 from HIV (>ENV_HV1H2 of 856 residues) over&nbsp; <i>Escherichia
coli</i> database <font size=-1> (CPU time ~3min + net delay)</font>.
<br>See <a href="#notes">technical</a> notes.</font></font>
<br>
<hr WIDTH="100%">

<br><form METHOD=POST enctype="multipart/form-data" ACTION="http://guitar.rockefeller.edu/~marcius/cgi-bin/clonerr.pl"><font face="Arial,Helvetica"><font size=+1><font color="#330033">Sequence
for which to run </font><b><font color="#000099">Clon</font><font color="#660000">Err</font></b><font color="#330033">:</font></font></font>
<br> <font color="#330033">Sequence title (optional):
<br><input TYPE=TEXT NAME="label" SIZE=30>
<br>Sequence: (<b>CAPITAL</b> letters!!!)
<br><textarea NAME="seq" ROWS=10 COLS=65 VALUE=""></textarea>
<p>
<font face="Arial,Helvetica"><font color="#330033">Choose a database for:&nbsp;<select NAME="db"><option>Your own DB<option></b><i>S.
cerevisiae<option>E. coli</select></i><br>
<font face="Arial,Helvetica"><font color="#330033">
If you have used your own database, please...<br>
enter here your two residue table <input type="file" name="inputfile2"><br>
enter here your three residue table <input type="file" name="inputfile3"><br>
enter here your four residue table <input type="file" name="inputfile4"><br>
<input TYPE=SUBMIT VALUE="Search"></form>
<p>

<hr WIDTH="100%">
<br><a NAME="notes"></a>
<br><font face="Arial,Helvetica"><font color="#330033">TECHNICAL NOTES:</font></font>
<br><font face="Arial,Helvetica"><font color="#330033"> Pre calculated aminoacid probability tables 
for <i>Echerichia coli</i> and <i>Saccharomyces cerevisiae</i> from Complete Genomes at NCBI 
(<a href="http://www.ncbi.nlm.nih.gov/Complete_Genomes/Ecoli/">http://www.ncbi.nlm.nih.gov/</a>).
Last update Nov, 1999. In a near
future the server will include other complete genomes.</font></font>
<br><font face="Arial,Helvetica"><font color="#330033">Clon-err program
has been compiled under UNIX machine.</font></font>
<br><a NAME="acce"></a>
<br><font face="Arial,Helvetica"><font color="#330033">THE "ACCEPTABILITY":</font></font>
<br><font face="Arial,Helvetica"><font color="#330033">The Acceptability
is a concept defined by the deviation between the real number in a database of a specific
sequence respect the expected number. Values near 0 indicates no variation
from expected and reality. Values under 0 indicates that the organism doesn't
use the specific sequence. Values over 0 indicates the over-expresion of
the specific sequence by the organism. To calculate the significance of the values a Z-score is introduced.</font></font>
