?? svm_align.html
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<P class=MsoNormal style="TEXT-ALIGN: center" align=center><SPAN
style="FONT-SIZE: 40pt">SVM<I
style="mso-bidi-font-style: normal"><SUP>align</SUP></I><SUP><o:p></o:p></SUP></SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center><SPAN style="FONT-SIZE: 18pt">Version V2.00<o:p></o:p></SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center><SPAN style="FONT-SIZE: 18pt"> <o:p></o:p></SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center>Authors:
Thorsten Joachims <<I style="mso-bidi-font-style: normal"><SPAN
style="COLOR: #993300">thorsten (a) joachims.org</SPAN></I>> & </P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center>Philip Zigoris
<<I style="mso-bidi-font-style: normal"><SPAN
style="COLOR: #993300">paz3 (a) cs.cornell.edu</SPAN></I>></P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center><U><SPAN
style="COLOR: #993300"><A href="javascript:if(confirm('http://www.cs.cornell.edu/ \n\nThis file was not retrieved by Teleport Pro, because it is addressed on a domain or path outside the boundaries set for its Starting Address. \n\nDo you want to open it from the server?'))window.location='http://www.cs.cornell.edu/'" tppabs="http://www.cs.cornell.edu/"><SPAN
style="COLOR: #993300">Dept. of Computer
Science</SPAN></A><o:p></o:p></SPAN></U></P>
<P class=MsoNormal style="TEXT-ALIGN: center" align=center><U><SPAN
style="COLOR: #993300"><A href="javascript:if(confirm('http://www.cornell.edu/ \n\nThis file was not retrieved by Teleport Pro, because it is addressed on a domain or path outside the boundaries set for its Starting Address. \n\nDo you want to open it from the server?'))window.location='http://www.cornell.edu/'" tppabs="http://www.cornell.edu/"><SPAN
style="COLOR: #993300">Cornell
University</SPAN></A><o:p></o:p></SPAN></U></P></TD>
<TD
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<P class=MsoNormal style="TEXT-ALIGN: center" align=center><SPAN
style="FONT-SIZE: 40pt"> <o:p></o:p></SPAN></P>
<P class=MsoNormal><A name=intro><SPAN style="FONT-SIZE: 13.5pt">This document
is organized as follows:</SPAN></A></P><SPAN style="mso-bookmark: intro"></SPAN>
<UL style="MARGIN-TOP: 0in" type=disc>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#intro"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">Introduction</SPAN></A>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#section1"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">Downloading and installing</SPAN></A>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#section4"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">Model file format</SPAN></A>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#section3"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">Input file format</SPAN></A>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#section5"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">Program usage</SPAN></A>
<LI class=MsoNormal style="mso-list: l3 level1 lfo3; tab-stops: list .5in"><A
href="#section7"><SPAN
style="FONT-SIZE: 13.5pt; COLOR: maroon">References</SPAN></A> </LI></UL>
<P class=MsoNormal> </P>
<P class=MsoNormal> </P>
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<P class=MsoNormal style="TEXT-ALIGN: center" align=center><B
style="mso-bidi-font-weight: normal"><SPAN
style="FONT-SIZE: 16pt; COLOR: #993300"> <U><o:p></o:p></U></SPAN></B></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 22pt">Introduction<o:p></o:p></SPAN></P>
<P class=MsoNormal>In sequence alignment, one often has a good idea, a priori,
of the appropriate values for various operations.<SPAN
style="mso-spacerun: yes"> </SPAN>For instance, your knowledge of
bio-chemistry might tell you that the probability of a match occurring is
greater than that of a protein being deleted from a sequence.<SPAN
style="mso-spacerun: yes"> </SPAN>Given these costs, one can find, by
dynamic programming, the optimal sequence of operations that aligns two
sequences.<SPAN style="mso-spacerun: yes"> </SPAN>The problem of Inverse
Sequence Alignment is, appropriately enough, the inverse of this.<SPAN
style="mso-spacerun: yes"> </SPAN>The learning problem can be generally
phrased as, given a collection of sequences with pairs labeled either 憇imilar?? 快捷鍵說明
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