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| <HTML>
| | Please refer to the [[Resources]] page. |
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| <TABLE CELLPADDING="0">
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| <TR>
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| <TD CLASS="bg">
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| <TABLE CELLPADDING="8" CELLSPACING="1">
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://molmovdb.org/molmovdb/morph">
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| <IMG SRC="./images/morph-icon.jpg" ALT="Morph Server"></A>
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| </TD>
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| <TD CLASS="description">
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| The <A CLASS="resource"
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| HREF="http://molmovdb.org/molmovdb/morph">Morph Server</A>
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| generates
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| a plausible pathway between two conformations of a protein or nucleic acid
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| structure.
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| A large number of statistics and several high-quality movies are
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| output.<br>
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| <SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A
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| HREF="/papers/molmovdb2">citation2</A> |
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| <A HREf="/papers/subject/motions">related</A> ]</SMALL>
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">
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| <IMG SRC="./images/express-logo.png" ALT="ExpressYourself"></A>
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| </TD>
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| <TD CLASS="description">
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| <A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/ExpressYourself">ExpressYourself</A> is an
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| interactive platform for
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| background correction, normalization, scoring, and quality assessment of
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| raw microarray data.<br>
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| <SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL>
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://spine.nesg.org">
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| <IMG SRC="./images/spine-icon.jpg" ALT="SPINE"></A>
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| </TD>
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| <TD CLASS="description">
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| <A CLASS="resource" HREF="http://spine.nesg.org">SPINE</A> is our
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| laboratory-information management
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| system (LIMS) for the <A CLASS="resource"
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| HREf="http://www.nesg.org">NorthEast Structural Genomics
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| Consortium</A>. The online version is restricted to consortium users, but
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| most of the code is
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| freely available for download.<br>
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| <SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A
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| HREF="/papers/spine2-nar">citation2</A> ]</SMALL>
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://pseudogene.org">
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| <IMG SRC="./images/pseudogene.png" ALT="Pseudogenes"></A>
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| </TD>
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| <TD CLASS="description">
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| <a class="resource" href="http://pseudogene.org">Pseudogene.org</a>
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| is a collection of resources related to our efforts to survey
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| eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage,
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| amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help
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| elucidate the relationships between pseudogene families across several
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| organisms.
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://tiling.gersteinlab.org/">
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| <IMG SRC="./images/tiling.png" ALT="Tiling"></A>
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| </TD>
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| <TD CLASS="description">
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| <a class="resource" href="http://tiling.gersteinlab.org/">Tiling</a>
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| is under construction.
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://networks.gersteinlab.org/genome/interactions/networks/">
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| <IMG SRC="./images/topnet.png" ALT="TopNet"></A>
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| </TD>
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| <TD CLASS="description">
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| <a class="resource" href="http://networks.gersteinlab.org/genome/interactions/networks/">TopNet</a>
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| is an automated web tool designed to calculate topological
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| parameters and compare different sub-networks for any given network.
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://geometry.molmovdb.org">
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| <IMG SRC="./images/volume.png" ALT="Protein Geometry"></A>
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| </TD>
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| <TD CLASS="description">
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| A number of programs for calculating properties of protein and nucleic
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| acid structures have
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| been collected into a <A CLASS="resource"
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| HREF="http://geometry.molmovdb.org">single
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| distribution</A>. Included are a library of utility functions for dealing
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| with structures,
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| and a convenient interactive command-line interpreter.
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| <SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL>
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">
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| <IMG SRC="./images/timeshift.png" ALT="Local Clustering"></A>
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| </TD>
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| <TD CLASS="description">
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| A new algorithm for <A CLASS="resource" HREF="http://bioinfo.mbb.yale.edu/expression/cluster">local
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| clustering of expression data</A> to find timeshifted and/or inverted
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| relationships is available as C source code.
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| <SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL>
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| </TD>
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| </TR>
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| <TR>
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| <TD CLASS="image" VALIGN="middle">
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| <A CLASS="image" HREF="/papers/xml/">
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| <IMG SRC="./images/papers.png" ALT="Papers"></A>
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| </TD>
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| <TD CLASS="description">
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| The <A CLASS="resource" HREF="/papers">publication listings</A> on our
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| site are automatically
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| generated based on data from the NCBI and local annotations stored in XML
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| format. The <A CLASS="resource" HREF="/papers/xml">code</A> which does
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| this is freely available
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| (some modification will be required for other sites).
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| </TD>
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| </TR>
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| </HTML>
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| </TABLE>
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| </TD></TR>
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| </TABLE>
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Please refer to the Resources page.
