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<DIV dir=ltr align=left><FONT size=2><SPAN class=428415612-09052007><SPAN
class=765594914-10052007><FONT face=Arial><SPAN class=074403006-29062007>Dear
all</SPAN>,</FONT></SPAN></SPAN></DIV>
<DIV>
<DIV><FONT face=Arial><SPAN class=428415612-09052007></SPAN></FONT> </DIV>
<DIV><SPAN class=428415612-09052007><SPAN class=765594914-10052007><FONT
face=Arial><SPAN class=074403006-29062007>I am new member of this mailing
list and I would like some advice of what should I do with my data. Maybe
it´s a wild guess but I just thought that spatial statistics can help me.
</SPAN>Here it goes:</FONT></SPAN></SPAN></DIV>
<DIV><FONT face=Arial><SPAN class=428415612-09052007><SPAN
class=765594914-10052007></SPAN></SPAN></FONT> </DIV>
<DIV><FONT size=+0><SPAN class=428415612-09052007><SPAN
class=765594914-10052007></SPAN><FONT face=Arial size=2>I am analysing data from
whole genome shotgun (WGS) sequencing of the cow and I am comparing
the obtained <SPAN class=074403006-29062007>numerous </SPAN><SPAN
class=074403006-29062007>small </SPAN>sequences to the cow reference genome
assembly. The WGS sequences are from a cow breed but the reference
genome is from another breed. I mapped the obtained sequences to
the reference genome with <SPAN class=074403006-29062007>an
</SPAN>algorithm <SPAN class=765594914-10052007>similar to BLAST </SPAN>and
now I have an output file with the score<SPAN class=074403006-29062007> (->
like a probability)</SPAN> of the alignment for each of my WGS sequences.
</FONT></DIV>
<DIV><SPAN class=428415612-09052007><FONT size=2><FONT face=Arial>In attachment
there is a picture with the genome <SPAN class=765594914-10052007>reference
</SPAN>sequence and my WGS sequences (called "tag" with light blue color)
and the correspondent scores. <SPAN class=128442709-07052007>In this picture we
just see a small portion of the chromosome 1 of the cow
genome.</SPAN></FONT></FONT></SPAN></DIV></SPAN></FONT>
<DIV><FONT face=Arial size=2><SPAN class=428415612-09052007></SPAN></FONT><FONT
size=+0><SPAN class=428415612-09052007><FONT size=2><SPAN
class=128442709-07052007></SPAN></FONT> </DIV>
<DIV class=qt style="DISPLAY: block"><SPAN class=128442709-07052007><FONT
face=Arial><FONT size=2><SPAN
class=428415612-09052007>Therefore</SPAN>, <SPAN class=428415612-09052007>I
would like to <SPAN class=765594914-10052007>know if it is possible to
use <SPAN class=074403006-29062007>some R packages that deal with
</SPAN><SPAN class=074403006-29062007>spatial analysis</SPAN> in order
to </SPAN></SPAN>see if there is any region of <SPAN
class=428415612-09052007>the genome</SPAN> that is statistically more dense in
these tags than another region<SPAN class=428415612-09052007>.<SPAN
class=765594914-10052007> </SPAN></SPAN></FONT></FONT></SPAN></DIV>
<DIV class=qt style="DISPLAY: block"><SPAN class=128442709-07052007><FONT
face=Arial size=2><SPAN
class=428415612-09052007></SPAN></FONT></SPAN> </DIV>
<DIV class=qt style="DISPLAY: block"><SPAN class=128442709-07052007><FONT
face=Arial size=2><SPAN class=428415612-09052007>Thanks for you
time.</SPAN></FONT></SPAN></DIV></SPAN></FONT></FONT></DIV>
<DIV> </DIV><BR><BR><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=2>Best regards</FONT><BR><BR><FONT
face="Arial, Helvetica, Geneva, Sans-Serif" size=2><B>João
Fadista</B></FONT><BR><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=2>Ph.d. student</FONT><BR><BR>
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<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" color=#003366
size=2><B>UNIVERSITY OF AARHUS</B></FONT></TD></TR>
<TR>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" color=#003366
size=2><B>Faculty of Agricultural Sciences</B></FONT></TD></TR>
<TR>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" size=1>Dept.
of Genetics and Biotechnology</FONT></TD></TR>
<TR>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>Blichers Allé 20, P.O. BOX 50</FONT></TD></TR>
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<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>DK-8830 Tjele</FONT></TD></TR>
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<TD width=60><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>Phone:</FONT></TD>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" size=1>+45
8999 1900</FONT></TD></TR>
<TR>
<TD width=60><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>Direct:</FONT></TD>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" size=1>+45
8999 1900</FONT></TD></TR>
<TR>
<TD width=60><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>E-mail:</FONT></TD>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" size=1><A
href="mailto:Joao.Fadista@agrsci.dk"><FONT
face="Arial, Helvetica, Geneva, Sans-Serif" color=#003366
size=1>Joao.Fadista@agrsci.dk</FONT></A></FONT></TD></TR>
<TR>
<TD width=60><FONT face="Arial, Helvetica, Geneva, Sans-Serif"
size=1>Web:</FONT></TD>
<TD><FONT face="Arial, Helvetica, Geneva, Sans-Serif" size=1><A
href="http://www.agrsci.org/"><FONT
face="Arial, Helvetica, Geneva, Sans-Serif" color=#003366
size=1>www.agrsci.org</FONT></A></FONT></TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE><FONT
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