Crover bioinformatics framework
Crover is a software framework that supports the development of Bioinformatics tools.
This framework has been designed by Fabien Campagne, PhD. while at different institutions
(Centre Charles Hermites, Spring 1998-September 1998;
Mount Sinai School of Medicine,
Department of Physiology and Biophysics, October 1998, June 2000,
Mount Sinai School of Medicine, Institute for Computational Biomedicine, July 2000-).
The Crover framework is expected to be used mainly by researchers who need to automate
tasks related to Bioinformatics. Crover is made of several packages that can be used
together or sometimes independently. An overview of the main packages is given below.
| representation |
Provides for the representation of sequences and annotations. This is a most central package of crover.
Other packages use the representation of sequences to perform treatments on the data.
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| imports |
Provides for the import of sequences from files (supported formats include SwissProt, Fasta, PIR, PDB).
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| util |
Provides a few classes which implement simple analysis tasks.
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| blast |
Provides classes to start a BLAST process and obtain a memory representation of the results.
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| tissue |
Supports the data management of tissue information. This package implements supporting classes and the command line tools included in TissueInfo. |
| domain2d |
Provides implementations of algorithms to draw residue-based diagrams of proteins.
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| clustalnet |
Provides access to clustalnet, a modified version of Clustal that offers a CORBA server.
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| CLI |
Provides general services needed by Command Line Interface programs. These services include: configuration of the environment through a property file, methods to parse options from the command line. |
A comparison of Crover with other bioinformatics framework has been presented at ISMB 2000.
A reprint is now available.
More information about Crover is available from our documentation area. Javadoc is used to
maintain the information offered in this area from the most stable version of Crover.
For more information about this framework, or to obtain a license,
please feel free to contact us.
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