Tools
From GersteinInfo
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| - | + | [http://molmovdb.org/molmovdb/morph Morph Server] generates a plausible pathway between two conformations of a protein or nucleic acid structure. A large number of statistics and several high-quality movies are output. | |
| - | generates | + | |
| - | a plausible pathway between two conformations of a protein or nucleic acid | + | |
| - | structure. | + | |
| - | A large number of statistics and several high-quality movies are | + | |
| - | output. | + | |
<SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A | <SMALL>[ <A HREF="/papers/morphs-nar">citation 1</A> | <A | ||
HREF="/papers/molmovdb2">citation2</A> | | HREF="/papers/molmovdb2">citation2</A> | | ||
<A HREf="/papers/subject/motions">related</A> ]</SMALL> | <A HREf="/papers/subject/motions">related</A> ]</SMALL> | ||
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| - | + | [http://bioinfo.mbb.yale.edu/ExpressYourself ExpressYourself] is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data. | |
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| - | interactive platform for | + | |
| - | background correction, normalization, scoring, and quality assessment of | + | |
| - | raw microarray data. | + | |
<SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL> | <SMALL>[ <A HREf="/papers/expressyourself">citation</A> ]</SMALL> | ||
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| - | + | [http://spine.nesg.org SPINE] is our laboratory-information management system (LIMS) for the [http://www.nesg.org NorthEast Structural Genomics Consortium]. The online version is restricted to consortium users, but most of the code is freely available for download.<br> | |
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| - | laboratory-information management | + | |
| - | system (LIMS) for the | + | |
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| - | Consortium | + | |
| - | most of the code is | + | |
| - | freely available for download.<br> | + | |
<SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A | <SMALL>[ <A HREF="/papers/spine-nar">citation1</A> | <A | ||
HREF="/papers/spine2-nar">citation2</A> ]</SMALL> | HREF="/papers/spine2-nar">citation2</A> ]</SMALL> | ||
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| - | + | [http://pseudogene.org Pseudogene.org] is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several | |
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| - | is a collection of resources related to our efforts to survey | + | |
| - | eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, | + | |
| - | amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help | + | |
| - | elucidate the relationships between pseudogene families across several | + | |
organisms. | organisms. | ||
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| - | + | [http://tiling.gersteinlab.org Tiling] is under construction. | |
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| - | + | [http://networks.gersteinlab.org/genome/interactions/networks/ TopNet] is an automated web tool designed to calculate topological parameters and compare different sub-networks for any given network. | |
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A number of programs for calculating properties of protein and nucleic | A number of programs for calculating properties of protein and nucleic | ||
| - | acid structures have | + | acid structures have been collected into a [http://geometry.molmovdb.org single distribution]. Included are a library of utility functions for dealing |
| - | been collected into a | + | with structures, and a convenient interactive command-line interpreter. |
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| - | distribution | + | |
| - | with structures, | + | |
| - | and a convenient interactive command-line interpreter. | + | |
<SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL> | <SMALL>[ <A HREF="/papers/subject/volumes">related papers</A> ]</SMALL> | ||
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| - | + | A new algorithm for [http://bioinfo.mbb.yale.edu/expression/cluster local clustering of expression data] to find timeshifted and/or inverted | |
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| - | A new algorithm for | + | |
| - | clustering of expression data | + | |
relationships is available as C source code. | relationships is available as C source code. | ||
<SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL> | <SMALL>[ <A HREF="/papers/timeshift-jmb">citation</A> ]</SMALL> | ||
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Revision as of 02:27, 2 June 2011
Morph Server generates a plausible pathway between two conformations of a protein or nucleic acid structure. A large number of statistics and several high-quality movies are output. [ <A HREF="/papers/morphs-nar">citation 1</A> | <A HREF="/papers/molmovdb2">citation2</A> | <A HREf="/papers/subject/motions">related</A> ]
ExpressYourself is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
[ <A HREf="/papers/expressyourself">citation</A> ]
SPINE is our laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download.
[ <A HREF="/papers/spine-nar">citation1</A> | <A HREF="/papers/spine2-nar">citation2</A> ]
Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several
organisms.
Tiling is under construction.
TopNet is an automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
A number of programs for calculating properties of protein and nucleic
acid structures have been collected into a single distribution. Included are a library of utility functions for dealing
with structures, and a convenient interactive command-line interpreter.
[ <A HREF="/papers/subject/volumes">related papers</A> ]
A new algorithm for local clustering of expression data to find timeshifted and/or inverted
relationships is available as C source code.
[ <A HREF="/papers/timeshift-jmb">citation</A> ]
<TR> <TD CLASS="image" VALIGN="middle"> <A CLASS="image" HREF="/papers/xml/"> <IMG SRC="./images/papers.png" ALT="Papers"></A> </TD> <TD CLASS="description"> The <A CLASS="resource" HREF="/papers">publication listings</A> on our site are automatically generated based on data from the NCBI and local annotations stored in XML format. The <A CLASS="resource" HREF="/papers/xml">code</A> which does this is freely available (some modification will be required for other sites).
</TD> </TR> </HTML>
</TABLE> </TD></TR> </TABLE>
