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

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.

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BioMed Central
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BMC Bioinformatics
Open Access
Software
SciDBMaker: new software for computer-aided design of
specialized biological databases
Riadh Hammami1, Abdelmajid Zouhir1, Karim Naghmouchi2, Jeannette Ben
Hamida1 and Ismail Fliss*3
Address: 1Unité de Protéomie Fonctionnelle & Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis,
Université El Manar, Tunisie, 2Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, T1J 4B1 Canada and 3Institut
des Nutraceutiques et des Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
Email: Riadh Hammami - Riadh.hammami@fst.rnu.tn; Abdelmajid Zouhir - azouheirb10@yahoo.fr;
Karim Naghmouchi - naghmouchik@agr.gc.ca; Jeannette Ben Hamida - benhamida_jeannette@yahoo.fr;
Ismail Fliss* - ismail.fliss@aln.ulaval.ca
* Corresponding author
Abstract
Background: 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.
Description: 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'.
Conclusion: 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.
Background
The exponential growth of molecular biology research in
recent decades has brought concomitant growth in the
number and size of databases used to interpret experi-
mental findings. For example, UniProtKB/Swiss-Prot
release 53.2, dated 26-06-07, contains 272,212 sequence
entries comprising 99,940,143 amino acids, abstracted
from 157,086 references [1]. A variety of protein sequence
databases exist, ranging from simple sequence repositor-
ies to expertly curated universal databases that cover all
Published: 25 February 2008
BMC Bioinformatics 2008, 9:121doi:10.1186/1471-2105-9-121
Received: 6 December 2007
Accepted: 25 February 2008
This article is available from: http://www.biomedcentral.com/1471-2105/9/121
© 2008 Hammami et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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species and in which the original sequence data are
enhanced by manual addition of further information in
each sequence record [2]. While all of these strive for com-
pleteness, the range of user interests is often beyond their
scope. This may reflect the user's wish to combine differ-
ent types of information or the inability of a single
resource to contain the complete details of every relevant
experiment. In addition, large databases with broad
domains tend to offer less detailed information than
smaller, more specialized, resources, with the result that
data from many resources may need to be combined to
provide a complete picture. There is a clear need to gather,
filter and critically evaluate this mass of information so
that it can be used with greater efficiency. Since scientists
are continually developing new specific databases to
enhance their understanding of biological processes, we
created SciDBMaker to provide a tool for easy building of
new specialized protein knowledge bases. This paper
describes the development of new stand-alone software,
Scientific DataBase Maker, for protein data analysis with
online and/or off-line access. The software interface
allows successive steps for sequence manipulation, start-
ing from user sequence search and homologous sequence
retrieval from the SwissProt databank, followed by physi-
cochemical profile calculations, multiple sequence align-
ments, phylogenic tree visualization and culminating in
database export/building. All steps are performed in an
interactive manner. Physical and chemical parameters,
rarely found in public databases, provide a helpful tool for
the analysis of a set of proteins and their calculation is
achieved in a direct and interactive manner, with off-line
access. SciDBMaker also processes a great number of
sequences simultaneously.
Implementation
Swiss-Prot format
The Swiss-Prot format has been described previously in
reference [3].
Physicochemical profiles
Protein families may be analyzed with the help of physic-
ochemical profiles such as amino acid composition
(acidic, basic, hydrophobic, polar, absent and common
amino acids), atomic composition, molecular weight [4],
theoretical pI [4,5], extinction coefficient [6], absorbance
at 280 nm, estimated half-life in mammalian cells, yeast
and E. coli [7,8], instability index [9], aliphatic index [10],
grand average of hydropathicity (GRAVY) [11] and pro-
tein-binding potential (Boman index) [12].
Integrated tools
The European Bioinformatics Institute provides the
Dbfetch tool for easy retrieval of entries from various data-
bases [13]. Entries may be imported online into SciDB-
Maker from the SwissProt database using Dbfetch. To find
similar sequences, the containers can be queried with
either proteins from the SwissProt database or user-
imported sequences, using the BLAST algorithm [14].
Multiple sequence alignments (MSA) are an essential tool
for predicting protein structure and function prediction,
phylogenic inference and other common tasks in
sequence analysis. To date, CLUSTALW is still the most
popular alignment tool. Since it is the method of choice
for biologists, CLUSTALW [15] was included in SciDB-
Maker for multiple sequence alignments. Generated trees
may be easily viewed using phylogenic tree visualization
software such as TREEVIEW [16].
Hardware and software specifications
The executable version of the SciDBMaker software can be
installed and run on a standard PC platform with a Win-
dows operating system. The software development was
done using Windows XP and tested with success on all
platforms, including Win 98, Win XP and Win vista. The
source code was written in Microsoft Visual Basic .NET
(2005). The environment is based upon the .NET Frame-
work library v2.0.
Results & discussion
Program description
The workflow diagram shown in Figure 1 and the follow-
ing discussion illustrate how the tool works. Figure 2 illus-
trates a typical user interface of the program. Users may
open files in Fasta or Swiss-Prot format, or import
sequence entries from the Swiss-Prot database. Users may
also use their own sequences, search for homologous
sequences entries in Swiss-Prot database using BLAST
algorithm and load selected entries into SciDBMaker (Fig.
3). The program will automatically extract available infor-
mation in Swiss-Prot entries and calculate physicochemi-
cal profiles for loaded proteins. Users may also choose the
information to be extracted and the properties to be calcu-
lated, as shown in Figure 4. The interface allows users to
filter, search, add, remove and update data rows as
required. An intuitive interface allows BLAST selection of
all user sequences. Similarly, sequences may be aligned
using the multiple alignment program ClustalW. Result-
ing trees may be shown using the phylogenic tree visuali-
zation software TREEVIEW, as proposed by SciDBMaker.
As a final step, data may be printed or saved in various file
formats. Sequences may be extracted into a Fasta format
file. The resulting data grid may be saved as an MS Excel
data sheet, as well as database files (XML, MS Access,
MySQL).

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Program runs
A database was developed using SciDBMaker. Named
BACTIBASE, this database has been previously described
in reference [17].
Conclusion
The stand-alone software SciDBMaker allows the extrac-
tion of protein data from the Swiss-Prot database,
sequence analysis comprising physicochemical profile
calculations, homologous sequence searches, multiple
sequence alignments and the building of new and more
specialized databases. Programs of this type compile
information with relative ease, update and compare vari-
ous data relevant to a given protein family and could solve
the problem of dispersed biological search results. Collec-
tion of a multitude of information regarding a given pro-
Workflow diagram
Figure 1
Workflow diagram.
?

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tein family allows the development of more coherent and
focused approaches to structure-function relationships,
thereby enhancing the development of theoretical con-
cepts in biological sciences.
Availability and requirements
The program runs on the PC platform with a Windows
operating system. The graphical environment needs the
.NET Framework library v2.0. This complement is availa-
ble for free download at the Microsoft website and comes
pre-installed in the majority of recent computers. An
installation package for SciDBMaker may be obtained
from the authors free of charge upon request. The SciDB-
Maker website is hosted by the Centre de Calcul El Kha-
warizmi CCK (Tunisia) and is available at http://
scidbmaker.pfba-lab.org. The SciDBMaker software is pro-
vided 'as is' with no guarantee or warranty of any kind and
is available for all non-commercial use. Any other use of
the software requires special permission from the primary
author.
Authors' contributions
RH programmed the software interface, performed the
implementation of physicochemical parameters and
drafted the manuscript. AZ participated in the design of
the study, interacted with RH to carry out the physico-
chemical data calculation and tested the program. KN
tested the program and contributed to the manuscript.
JBH oversaw the project and helped define user require-
ments. IF conceived the study, participated in its design
and coordination and helped to draft the manuscript. All
authors read and approved the final manuscript.
User interface
Figure 2
User interface.

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A typical Blast result window
Figure 3
A typical Blast result window.
Preference display columns
Figure 4
Preference display columns.