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<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>Nagesh,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>Vector NTI's (windows only) AlignX module
supports your needs quite nicely (though not in a high throughput
fashion). Version 10 is now free to academics (!), though getting
registered is a bit of a bear. </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>Some researchers here at the Stowers Institute used it for
amping up a lizard gene based on chicken aligned with (was it?) mouse. For
further specificity, they designed nested degenerate primer pairs (if I remember
correctly).</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>AlignX can import precomputed alignments too (but only in
MAF format).</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><FONT face=Arial><FONT size=2><FONT color=#0000ff><SPAN
class=151340616-23022006>Let us know what you do.</SPAN><SPAN
class=151340616-23022006></DIV></SPAN></FONT></FONT></FONT>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>The following is from their Help file, and might help you
decide if the weighty install is worth your effort:</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>The Alignment PCR feature in Vector NTI allows you to
design PCR primers for amplifying a region of aligned DNA/RNA molecules. Using
this feature, you can design primer pair sets that will amplify any of the
DNA/RNA molecules in a specified alignment. In this type of PCR analysis, the
molecules are first aligned in AlignX and the alignment is subsequently
analyzed using the Alignment PCR feature in Vector NTI.<BR>The basic procedure
for performing an Alignment PCR analysis consists of the following
steps:</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>1. Define the set of DNA/RNA molecules you want to
use for Alignment PCR analysis.</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>2. Align the set of molecules in
AlignX.</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>3. Select a region of the AlignX alignment for which
Alignment PCR will be run.</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>4. Define the Alignment PCR
parameters.</FONT></SPAN></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>5. Perform the Alignment PCR
analysis.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV></BLOCKQUOTE>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>From another page in the help file (Alignment PCR
parameters), I quote additionally:</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>Primer/Every Molecule Set the minimum overall
similarity and 3’ end similarity for the primer with every molecule in the
alignment</FONT></SPAN></DIV></BLOCKQUOTE><SPAN class=151340616-23022006>
<P dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2>Cheers,</FONT></SPAN></P>
<P dir=ltr align=left><SPAN class=151340616-23022006></SPAN><FONT face=Arial
color=#0000ff size=2>Malcolm Cook - </FONT><A
href="mailto:mec@stowers-institute.org"><FONT face=Arial
size=2>mec@stowers-institute.org</FONT></A><FONT face=Arial color=#0000ff
size=2> - 816-926-4449<BR>Database Applications Manager -
Bioinformatics<BR>Stowers Institute for Medical Research - Kansas City, MO
USA </FONT></P>
<P dir=ltr align=left><FONT face=Arial color=#0000ff
size=2></FONT><BR></P></SPAN>
<DIV dir=ltr align=left><SPAN class=151340616-23022006><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV><BR>
<BLOCKQUOTE
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT face=Arial
color=#0000ff size=2>
<HR tabIndex=-1>
From: bio_bulletin_board-bounces+mec=stowers-institute.org@bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org@bioinformatics.org]
On Behalf Of Maximilian Haeussler<BR>Sent: Wednesday, February 22, 2006 7:56
PM<BR>To: The general forum at Bioinformatics.Org<BR>Subject: Re: [BiO BB]
Designing degenerate primers<BR><BR></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT></DIV><FONT face=Arial
color=#0000ff size=2>forgot to forward to the list: <BR>you don't have to do
the sequences alignment yourself. on </FONT><A
onclick="return top.js.OpenExtLink(window,event,this)"
href="http://genome-test.soe.ucsc.edu/" target=_blank><FONT face=Arial
size=2>genome-test.soe.ucsc.edu </FONT></A><FONT face=Arial color=#0000ff
size=2>you'll find multiple alignments of 12 mammalian species (switch on
track "MultiZ 10 way" or "MultiZ 12 way"). You can extract alignments with
"Table Browser" - "MultiZ 10 Way" - Download as maf (or fasta?). <BR><BR>Take
care,<BR>Max<BR><BR></FONT>
<DIV><SPAN class=gmail_quote><FONT face=Arial color=#0000ff size=2>On
22/02/06, Nagesh Chakka <</FONT><A
href="mailto:nagesh.chakka@anu.edu.au"><FONT face=Arial size=2>
nagesh.chakka@anu.edu.au</FONT></A><FONT face=Arial color=#0000ff size=2>>
wrote:</FONT></SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><FONT
face=Arial color=#0000ff size=2>Hi all,<BR>I need to design primers to "fish
out" the region of interest from <BR>reptilian genomic sequence. I donot
have the reptilian gDNA sequence<BR>information to design the primer with
exact sequence. Hence I thought of<BR>designing degenerate primers based on
the available sequence information <BR>(eutherian mammal, marsupial,
amphibian). Are there any available<BR>programs which does this kind of
primer design or that I need to perform<BR>a multiple sequence alignment and
look for the most conserved region and <BR>design primer with that.<BR>Any
advice is greatly
appreciated.<BR>Thanks<BR>Nagesh<BR>_______________________________________________<BR>Bioinformatics.Org
general forum - </FONT><A
href="mailto:BiO_Bulletin_Board@bioinformatics.org"><FONT face=Arial size=2>
BiO_Bulletin_Board@bioinformatics.org</FONT></A><BR><A
href="https://bioinformatics.org/mailman/listinfo/bio_bulletin_board"><FONT
face=Arial
size=2>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board</FONT></A><BR></BLOCKQUOTE></DIV><BR><BR
clear=all><BR><FONT face=Arial color=#0000ff size=2>-- <BR>Maximilian
Haeussler, <BR>CNRS Gif-sur-Yvette, Paris<BR>tel: +33 6 12 82 76 16<BR>icq:
3825815 -- msn: </FONT><A
href="mailto:maximilian.haeussler@hpi.uni-potsdam.de"><FONT face=Arial
size=2>maximilian.haeussler@hpi.uni-potsdam.de</FONT></A><FONT face=Arial
color=#0000ff size=2> <BR>skype: maximilianhaeussler
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