[Bioperl-l] Does pWS work with DNA sequence?
Brian Osborne
brian_osborne@cognia.com
Wed, 7 Aug 2002 08:09:24 -0400
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Shukui,
The pSW module doesn't work with nucleotide sequence. I believe that this is
stated in the module's documentation, in bptutorial.pl, and in the FAQ. For
advice on Smith-Waterman and nucleotide sequences take a look at water, in
the EMBOSS package, it's described in bptutorial.pl, or in the FAQ.
Brian O.
-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Shukui Guan
Sent: Tuesday, August 06, 2002 5:48 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Does pWS work with DNA sequence?
Hi there,
I am new to this exciting area. I am trying to align two DNA sequence, so I
installed BioPerl at my home directory and modified one of the sample
scripts (psw.pl) as follow:
#!/usr/bin/perl
use lib "/users/u/4/sguan/bioperl/blib/arch";
use lib "/users/u/4/sguan/bioperl/blib/lib";
use lib "/nfs/disk100/pubseq/wise/PerlMod/";
use Bio::Tools::pSW;
use Bio::Seq;
use Bio::SimpleAlign;
use Bio::AlignIO;
# for legibility - write with newlines and then strip them!
print "\nNow let stop\n\n";
$tseq = 'GGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGA
AGAATTCCAGGTGTAGCGGTGAAAT';
$tseq =~ s/[^A-Z]//g;
$seq1 = Bio::Seq->new(-id=>'roa1_human',-seq=>$tseq);
$tseq =
'GAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAANCAGCTTGCTGNTTNGCTGACGA
GTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGA';
$tseq =~ s/[^A-Z]//g;
$seq2 = Bio::Seq->new(-id=>'roa1_drome',-seq=>$tseq);
# Now make an Alignment Factory with blosum62 as a matrix
# gap -12 and ext -2
#
$fac = Bio::Tools::pSW->new(-matrix => 'blosum62.bla',-gap => 12, -ext =>
2);
#
# run seq1 vs seq2 and seq1 vs seq3 and write the output direct
# to stdout using the 'pretty' method
#
$fac->align_and_show($seq1,$seq2,STDOUT);
print "Next alignment\n";
##################################
Unfortunately, it did not work. Here is the error message.
Now let stop
Warning Error
Sequence roa1_human is not typed as protein... ignoring!
Warning Error
Sequence roa1_drome is not typed as protein... ignoring!
Warning Error
Could not evaluate these sequences Sequence type [66][Dna]
Evaluation
type [65][Protein]
------------- EXCEPTION -------------
MSG: Unable to build an alignment
STACK Bio::Tools::pSW::align_and_show
/users/u/4/sguan/bioperl/blib/lib/Bio/Tool
s/pSW.pm:339
STACK toplevel psw.pl:44
So what is going on? Anyone can help?
Stephen G
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<div class=3DSection1>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Sh=
ukui,<o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><!=
[if =
!supportEmptyParas]> <![endif]><o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Th=
e pSW
module doesn’t work with nucleotide sequence. I believe that this =
is stated in
the module’s documentation, in bptutorial.pl, and in the FAQ. For =
advice on
Smith-Waterman and nucleotide sequences take a look at water, in the =
EMBOSS
package, it’s described in bptutorial.pl, or in the =
FAQ.<o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><!=
[if =
!supportEmptyParas]> <![endif]><o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Br=
ian O.<o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><!=
[if =
!supportEmptyParas]> <![endif]><o:p></o:p></span></font></span></p>
<p class=3DMsoNormal><span class=3DEmailStyle15><font size=3D2 =
color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><!=
[if =
!supportEmptyParas]> <![endif]><o:p></o:p></span></font></span></p>
<p class=3DMsoNormal style=3D'margin-left:.5in'><font size=3D2 =
color=3Dblack
face=3DTahoma><span =
style=3D'font-size:10.0pt;font-family:Tahoma;color:black'>-----Original
Message-----<br>
<b><span style=3D'font-weight:bold'>From:</span></b> =
bioperl-l-admin@bioperl.org
[mailto:bioperl-l-admin@bioperl.org]<b><span =
style=3D'font-weight:bold'>On Behalf
Of </span></b>Shukui Guan<br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Tuesday, August 06, =
2002
5:48 PM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> =
bioperl-l@bioperl.org<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> [Bioperl-l] Does =
pWS work
with DNA sequence?</span></font></p>
<p class=3DMsoNormal style=3D'margin-left:.5in'><font size=3D3 =
face=3D"Times New Roman"><span
style=3D'font-size:12.0pt'><![if =
!supportEmptyParas]> <![endif]><o:p></o:p></span></font></p>
<p class=3DMsoNormal =
style=3D'mso-margin-top-alt:1.5pt;margin-right:0in;margin-bottom:
0in;margin-left:37.5pt;margin-bottom:.0001pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:7.5pt;font-family:"MS =
Sans Serif";
color:black'>Hi there,</span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:7.5pt;font-family:"MS =
Sans Serif";
color:black'>I am new to this exciting area. I am trying to align =
two DNA
sequence, so I installed BioPerl at my home directory and modified one =
of the
sample scripts (psw.pl) as follow:</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>#!/usr/bin/perl</span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>use lib "/users/u/4/sguan/bioperl/blib/arch";<br>
use lib "/users/u/4/sguan/bioperl/blib/lib";<br>
use lib =
"/nfs/disk100/pubseq/wise/PerlMod/";</span></font><font
size=3D1 color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;
font-family:"MS Sans =
Serif";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p=
>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>use Bio::Tools::pSW;</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'><br>
use Bio::Seq; <br>
use Bio::SimpleAlign;<br>
use Bio::AlignIO;</span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'># for legibility - write with newlines and then strip =
them!<br>
print "\nNow let stop\n\n";<br>
$tseq =3D =
'GGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGA<br>
AGAATTCCAGGTGTAGCGGTGAAAT';</span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>$tseq =3D~ s/[^A-Z]//g;</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>$seq1 =3D =
Bio::Seq->new(-id=3D>'roa1_human',-seq=3D>$tseq);</span></font><=
font
size=3D1 color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;
font-family:"MS Sans =
Serif";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p=
>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>$tseq =3D =
'GAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAANCAGCTTGCTGNTTNGCTGACGA<=
br>
GTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGA';</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>$tseq =3D~ s/[^A-Z]//g;</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>$seq2 =3D =
Bio::Seq->new(-id=3D>'roa1_drome',-seq=3D>$tseq);</span></font><=
font
size=3D1 color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;
font-family:"MS Sans =
Serif";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p=
>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'># Now make an Alignment Factory with blosum62 as a =
matrix<br>
# gap -12 and ext -2<br>
#<br>
$fac =3D Bio::Tools::pSW->new(-matrix =3D> 'blosum62.bla',-gap =
=3D> 12, -ext
=3D> 2);</span></font><font size=3D1 color=3Dblack face=3D"MS Sans =
Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'><br>
#<br>
# run seq1 vs seq2 and seq1 vs seq3 and write the output direct <br>
# to stdout using the 'pretty' method<br>
#</span></font><font size=3D1 color=3Dblack face=3D"MS Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'><br>
$fac->align_and_show($seq1,$seq2,STDOUT);<br>
print "Next alignment\n";</span></font><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>##################################</span></font><font =
size=3D1
color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;font-family:"MS Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>Unfortunately, it did not work. Here is the error =
message.</span></font><font
size=3D1 color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;
font-family:"MS Sans =
Serif";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p=
>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>Now let stop</span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>Warning Error<br>
Sequence roa1_human is not =
typed as
protein... ignoring!</span></font><font size=3D1 color=3Dblack =
face=3D"MS Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>Warning Error<br>
Sequence roa1_drome is not =
typed as
protein... ignoring!</span></font><font size=3D1 color=3Dblack =
face=3D"MS Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'>Warning Error<br>
Could not evaluate these =
sequences
Sequence type [66][Dna] Evaluation<br>
type [65][Protein]<br>
------------- EXCEPTION -------------<br>
MSG: Unable to build an alignment<br>
STACK Bio::Tools::pSW::align_and_show
/users/u/4/sguan/bioperl/blib/lib/Bio/Tool<br>
s/pSW.pm:339<br>
STACK toplevel psw.pl:44 </span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:7.5pt;font-family:"MS =
Sans Serif";
color:black'>So what is going on? Anyone can =
help?</span></font><font
size=3D1 color=3Dblack face=3D"MS Sans Serif"><span =
style=3D'font-size:8.0pt;
font-family:"MS Sans =
Serif";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p=
>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:7.5pt;font-family:"MS =
Sans Serif";
color:black'>Stephen G</span></font><font size=3D1 color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>
<p class=3DMsoNormal style=3D'margin-left:37.5pt'><font size=3D1 =
color=3Dblack
face=3D"MS Sans Serif"><span style=3D'font-size:8.0pt;font-family:"MS =
Sans Serif";
color:black'> </span></font><font size=3D1 color=3Dblack face=3D"MS =
Sans Serif"><span
style=3D'font-size:8.0pt;font-family:"MS Sans =
Serif";color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>
</div>
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