SciDBMaker: New software for computer-aided design of specialized biological databases

Unité de Protéomie Fonctionnelle & Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université El Manar, Tunisie.
BMC Bioinformatics (Impact Factor: 2.58). 02/2008; 9(1):121. DOI: 10.1186/1471-2105-9-121
Source: DBLP


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.

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Available from: Ismail Fliss, Jul 07, 2015
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    • "and Apache (v2.2.2.1), while the Web interface was implemented with PHP (v5.2.17). Sequences were retrieved in SciDBMaker (Hammami et al. 2008), compiled and the resulting tables exported to the MySQL server. MilkAMP includes numerous tools for sequence analysis, such as homology search (BLAST v2.2.15 (Altschul et al. 1997), FASTA v35.04 (Pearson and Lipman 1988) and Smith– Waterman v35.04 (Pearson and Lipman 1988)), multiple sequence alignment (ClustalW v2.10 (Larkin et al. 2007), MUSCLE v3.6 (Edgar 2004)), Hidden Markov Models (HMMER v2.3.2 (Durbin et al. 1998)), and physicochemical profile analyzer. "
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    • "All microbiological information was collected from the literature by PubMed search. A physicochemical dataset was designed using SciDBMaker [9] and then provided with empirical formula, mass, length, isoelectric point, net charge, the number of basic, acidic, hydrophobic and polar residues, hydropathy index, binding potential index, instability index, aliphatic index, half-life in mammalian cells, yeast and E. coli, cysteine and glycine content, extinction coefficient, absorbance at 280 nm, absent and most prevalent amino acids, secondary (α-helix or β-strand) and tertiary structure (when available), physical method used for structural determination (e.g. NMR spectroscopy or X-ray diffraction) and critical residues for activity, whenever information was available. "
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