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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi James,</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I re-ran your query on our system and on the NCBI website,
and found that our results matched NCBI’s online results</span></font><font
size=2 face="Comic Sans MS"><span style='font-size:10.0pt;font-family:"Comic Sans MS"'> </span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>even after
an NT database refresh</span></font><font size=2 face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS"'>. </span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> To give you
an idea of the differences, here are snippets of the summaries:</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>NCBI online:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
Score
E</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sequences producing significant
alignments:
(Bits)
Value</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|58696605|emb|BX324134.11| Zebrafish DNA sequence
from clon... 1283 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|58037056|emb|CR382292.9| Zebrafish DNA sequence
from clone... 1235 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|66766177|emb|CR752650.10| Zebrafish DNA sequence
from clon... 1128 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|78611226|emb|CR788303.14| Zebrafish DNA sequence
from clon... 1011 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|42734280|emb|BX088536.8| Zebrafish DNA sequence
from clone... 993 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|46241816|emb|BX088654.11| Zebrafish DNA sequence
from clon... 987 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|42558145|emb|AL929105.27| Zebrafish DNA sequence
from clon... 950 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|38143448|emb|BX005158.8| Zebrafish DNA sequence
from clone... 930 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|60219425|emb|BX666059.13| Zebrafish DNA sequence
from clon... 928 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|63025084|emb|BX511111.16| Zebrafish DNA sequence
from clon... 866 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|59891285|emb|BX927256.13| Zebrafish DNA sequence
from clon... 864 0.0</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPT results:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
Score E</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sequences producing significant
alignments:
(bits)
Value</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|58696605|emb|BX324134.11| Zebrafish DNA sequence from
clone D... 1283 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|58037056|emb|CR382292.9| Zebrafish DNA sequence from
clone DK... 1235 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|66766177|emb|CR752650.10| Zebrafish DNA sequence from
clone C... 1128 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|78611226|emb|CR788303.14| Zebrafish DNA sequence from
clone D... 1011 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|42734280|emb|BX088536.8| Zebrafish DNA sequence from
clone </span></font><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>CH.</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>.. 993
0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|46241816|emb|BX088654.11| Zebrafish DNA sequence from
clone C... 987 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|42558145|emb|AL929105.27| Zebrafish DNA sequence from
clone C... 950 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|38143448|emb|BX005158.8| Zebrafish DNA sequence from
clone DK... 930 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|60219425|emb|BX666059.13| Zebrafish DNA sequence from
clone D... 928 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|63025084|emb|BX511111.16| Zebrafish DNA sequence from
clone R... 866 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gi|59891285|emb|BX927256.13| Zebrafish DNA sequence from
clone C... 864 0.0</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Your results:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
Score
E</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sequences producing significant alignments:
(bits)
Value</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|BX324134.11| Zebrafish DNA sequence from clone
DKEY-103K8 in... 1074 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|CR788303.14| Zebrafish DNA sequence from clone
DKEY-178E17 i... 1031 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|BX088654.11| Zebrafish DNA sequence from clone
CH211-195H6 i... 995 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|AL929105.27| Zebrafish DNA sequence from clone
CH211-142D6 i... 971 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|CR752650.10| Zebrafish DNA sequence from clone
CH211-140L3 i... 955 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|BX005158.8| Zebrafish DNA sequence from clone DKEY-222N6
in ... 946 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|BX511111.16| Zebrafish DNA sequence from clone RP71-62I8
in ... 872 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|AL929548.8| Zebrafish DNA sequence from clone
CH211-159E17, ... 870 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|BX957309.6| Zebrafish DNA sequence from clone
CH211-113P19 i... 860 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|AL844150.6| Zebrafish DNA sequence from clone
DKEY-246K2, co... 842 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>emb|CR847981.15| Zebrafish DNA sequence from clone
CH211-195H23 ... 769 0.0 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>----------------------------------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>It may be that the only differences are those of the NT
database, as MPT’s initial results were still very similar to
NCBI’s results, with the only alignments missing being those that were
found when the NT database was refreshed. It is still unclear to me why your
results are markedly different from NCBI and MPT, but it’s probably
related to search parameters or some other difference. </span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face="Comic Sans MS"><span style='font-size:
10.0pt;font-family:"Comic Sans MS"'>The</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> complete results files have been
posted to your user results directory on <a href="http://www.mptbiotech.com/">www.mptbiotech.com</a>
if you wish to examine them more closely. </span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thank you</span></font><font size=2 face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS"'> for </span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>challenging
us. We want to make sure users are confident enough to be able to publish
their results if they so choose. Feel free to contact us (or me directly)
with any further concerns or questions.</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Nick Robertson</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>==========================</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Principal Engineer</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Massively Parallel Technologies, Inc.</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>(303) 926-1231</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>(303) 915-4609 (cell)</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>email: nick@massivelyparallel.com</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>www.massivelyparallel.com</span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>==========================</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
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