SciDBMaker: new software for computer-aided design of specialized biological databases
Identifieur interne : 000053 ( Main/Exploration ); précédent : 000052; suivant : 000054SciDBMaker: new software for computer-aided design of specialized biological databases
Auteurs : Riadh Hammami [Tunisie] ; Abdelmajid Zouhir [Tunisie] ; Karim Naghmouchi ; Jeannette Ben Hamida [Tunisie] ; Ismail Fliss [Canada]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2008.
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English descriptors
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Abstract
The exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive for completeness, the range of user interests is often beyond their scope. Large databases covering a broad range of domains tend to offer less detailed information than smaller, more specialized resources, often creating a need to combine data from many sources in order to obtain a complete picture. Scientific researchers are continually developing new specific databases to enhance their understanding of biological processes.
In this article, we present the implementation of a new tool for protein data analysis. With its easy-to-use user interface, this software provides the opportunity to build more specialized protein databases from a universal protein sequence database such as Swiss-Prot. A family of proteins known as bacteriocins is analyzed as 'proof of concept'.
SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results.
Url:
DOI: 10.1186/1471-2105-9-121
PubMed: 18298861
PubMed Central: 2267701
Affiliations:
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(méthodes)</term><term>Systèmes de gestion de bases de données (MeSH)</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Information Storage and Retrieval</term><term>Molecular Biology</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie moléculaire</term><term>Mémorisation et recherche des informations</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Database Management Systems</term><term>Databases, Genetic</term><term>Software</term><term>Software Design</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Bases de données génétiques</term><term>Conception de logiciel</term><term>Logiciel</term><term>Systèmes de gestion de bases de données</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive for completeness, the range of user interests is often beyond their scope. Large databases covering a broad range of domains tend to offer less detailed information than smaller, more specialized resources, often creating a need to combine data from many sources in order to obtain a complete picture. Scientific researchers are continually developing new specific databases to enhance their understanding of biological processes.</p></sec><sec><title>Description</title><p>In this article, we present the implementation of a new tool for protein data analysis. With its easy-to-use user interface, this software provides the opportunity to build more specialized protein databases from a universal protein sequence database such as Swiss-Prot. A family of proteins known as bacteriocins is analyzed as 'proof of concept'.</p></sec><sec><title>Conclusion</title><p>SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li><li>Tunisie</li></country></list><tree><noCountry><name sortKey="Naghmouchi, Karim" sort="Naghmouchi, Karim" uniqKey="Naghmouchi K" first="Karim" last="Naghmouchi">Karim Naghmouchi</name></noCountry><country name="Tunisie"><noRegion><name sortKey="Hammami, Riadh" sort="Hammami, Riadh" uniqKey="Hammami R" first="Riadh" last="Hammami">Riadh Hammami</name></noRegion><name sortKey="Ben Hamida, Jeannette" sort="Ben Hamida, Jeannette" uniqKey="Ben Hamida J" first="Jeannette" last="Ben Hamida">Jeannette Ben Hamida</name><name sortKey="Zouhir, Abdelmajid" sort="Zouhir, Abdelmajid" uniqKey="Zouhir A" first="Abdelmajid" last="Zouhir">Abdelmajid Zouhir</name></country><country name="Canada"><noRegion><name sortKey="Fliss, Ismail" sort="Fliss, Ismail" uniqKey="Fliss I" first="Ismail" last="Fliss">Ismail Fliss</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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