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The GeneHuggers toolkit contains over 70 individual programs
which can be used in the construction of customized bioinformatics applications.
In order to accomodate a wide variety of scientific interests,
each basic function with respect to data mining and sequence analysis
has been modularized into a separate executable.
Each GeneHuggers program utilizes a common datatype so that the output
of one module can be used as input to another module.
Complex queries are composed using this finite set of tools by
combining them into an infinite number of serial assemblies.
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This data type, hereafter refered to as GeneHuggers hit I/O, ghio,
is an ASCII text representation of numerical data
compatible with all standard UNIX tools like grep, sort, sed, awk, vi, more, etc...
The databases that can be mined with GeneHuggers include:
UniGene, LocusLink, and any GenBank formatted sequence flatfile
including the RefSeq genome contigs.
In addition, GeneHuggers supports FASTA/FASTN file formats so that
either non-public data or modified subsets of the public data can
also be used with the toolkit.
The ability to generate and use FASTA/N formatted sequence files with
GeneHuggers also enables the use of BLAST and other sequence analysis
programs in the construction of GeneHuggers applications.
Common programs utilized in GeneHuggers applications currently include:
BLAST, HMMR, MEME, MAST, and CLUSTALW.
GeneHuggers has tools which can create input files for these programs
as well as parsers which can transform the output reports of these
programs back into ghio.
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There are many aspects of GeneHuggers that are new for most biologists
and their presentation is an organisational nightmare for me, the sole
person responsible for creating, developing, testing, and documenting
this project. If you have specific issues that are not addressed by this
web site, please check the ftp site for the manual. If you have sucessfully
installed GeneHuggers at your own site and are happy/unhappy with it or
have additional questions not covered in the documentation,
please email me Jason S. Iacovoni, jiaco@scripps.edu.
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GeneHuggers is avaiable for FREE, under the terms and conditions of the
GNU General Public License.
It is my intention that programers interested in extending the functionality
of GeneHuggers to include other databases and other applications do so
in a manner consistent with the GNU General Public License.
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