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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Sinead,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks a lot for your quick response. I
found a copy of prima in an older version of EMBOSS download.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>My intention is to use prima for
sequencing primer selection. However, after I tried a few sequences, from which
I picked primers before, prima picked no forward sequencing primer at all. An
example:</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>INPUT SUMMARY</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>*************</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Prima of from positions 50 to 600 bps</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>PRIMER CONSTRAINTS:</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>PRIMA DOES NOT ALLOW PRIMER SEQUENCE
AMBIGUITY OR DUPLICATE PRIMER ENDPOINTS</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Primer size range is 18-22</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Primer GC content range is 0.40-0.55</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Primer melting Temp range is 53.00 - 75.00
C</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>PRODUCT CONSTRAINTS:</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Product GC content range is 0.40-0.55</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Salt concentration is 50.00 (mM)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>DNA concentration is 50.00 (nM)</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Targeted range to amplify is from 50 to
600</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<div style='border:none;border-bottom:dotted windowtext 3.0pt;padding:0in 0in 1.0pt 0in'>
<p class=MsoNormal style='border:none;padding:0in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>PRIMER/PRODUCT
PAIR CALCULATIONS & OUTPUT</span></font></p>
</div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Sequence is:</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>CCTATAGGGCGGCCGCGAATTCGGCACGAGGCTGCAACAGCAGACCAAGCACCGCGGCGGACCCAGGCAAGCACGGAACAAGCTGAGACGGATGATAATATGGATACAAAATCTATTCTAGAAGAACTTCTTCTCAAAAGATCACAGCAAAAG</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>AAGAAAATGTCACCAAATAATTACAAAGAACGGCTTTTTGTTTTGACCAAAACAAACCTTTCCTACTATGAATATGACAAAATGAAAAGGGGCAGCAGAAAAGGATCCATTGAAATTAAGAAAATCAGATGTGTGGAGAAAGTAAATCTCGAG</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>GAGCAGACGCCTGTAGAGAGACAGTACCCATTTCAGATTGTCTATAAAGATGGGCTTCTCTATGTCTATGCATCAAATGAAGAGAGCCGAAGTCAGTGGTTGAAAGCATTACAAAAAGAGATAAGGGGTAACCCCCACCTGCTGGTCAAGTAC</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>CATAGTGGGTTCTTCGTGGACGGGAAGTTCCTGTGTTGCCAGCAGAGCTGTAAAGCAGCCCCAGGATGTACCCTCTGGGAAGCATATGCTAATCTGCATACTGCAGTCAATGAAGAGAAACACAGAGTTCCCACCTTCCCAGACAGAGTGCTG</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>AAGATACCTCGGGCAGTTCCTGTTCTCAAAATGGATGCACCATCTTCAAGTACCACTCTAGCCCAATATGACAACGAATCAAAGAAAAACTATGGCTCCCAGCCACCATCTTCAAGTACCAGTCTAGCGCAATATGACAGCAACTCAAAGAAA</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>ATCTATGGCTCCCAGCCAAACTTCAACATGCAGTATATTCCAAGGGAAGACTTCCCTGACTGGTGGCAAGTAAGAAAA</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Did you miss something in parameters? Any
idea? Thanks again for your help.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Cheers, -Wei</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> Sinéad O'Leary
[mailto:oleary@genome.wi.mit.edu] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, September 02, 2003
1:39 PM<br>
<b><span style='font-weight:bold'>To:</span></b> Wei Tao<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: prima</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi - I no longer work on the EMBOSS project but you
can find any information and the latest downloads from the website below. I'm
not sure if the prima program is still in the package, but there are another
primer related programs called 'primers' and 'primersearch'. </span></font></p>
<p style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Version 2.7.0 is available from: </span></font></p>
<p style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <a
href="http://www.uk.embnet.org/Software/EMBOSS">http://www.uk.embnet.org/Software/EMBOSS</a>
<br>
<a href="ftp://ftp.uk.embnet.org/pub/EMBOSS">ftp://ftp.uk.embnet.org/pub/EMBOSS</a>
</span></font></p>
<p style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>There is an emboss mailing list where questions on any
of the programs or installations are answered: <emboss@embnet.org> This
may also be useful to you. </span></font></p>
<p style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>hope this helps, <br>
Sinéad. <br>
<br>
<br>
</span></font></p>
<p style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Wei Tao wrote: </span></font></p>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' TYPE=CITE>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Hi Sinead,</span></font></p>
</div>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>I wonder where can I find a copy of
prima for download? Your help is deeply appreciated.</span></font> </p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Thanks!</span></font> </p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>-Wei</span></font></p>
</blockquote>
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