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Cry-Bt identifier: A biological database for PCR detection

of Cry genes present in transgenic plants
Vinay Kumar Singh, Sonu Ambwani, Soma Marla*, Anil Kumar

Bioinformatics Centre, Molecular Biology & Genetic Engineering, CBS&H, G.B. Pant University of Agriculture & Technology, Pantnagar,
Uttarakhand.263145, India: Soma Marla - E-mail: [email protected]; *Corresponding author

Received June 14, 2009; Revised August 01, 2009; Accepted September 11, 2009; Published October 23, 2009
Abstract:
We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic
crops. The tool also helps in detection of transformed Cry genes from Bacillus thuringiensis present in transgenic plants by providing
suitable designed primers for PCR identification of these genes. The tool designed based on relational database model enables easy retrieval
of information from the database with simple user queries. The tool also enables users to access related information about Cry genes present
in various databases by interacting with different sources (nucleotide sequences, protein sequence, sequence comparison tools, published
literature, conserved domains, evolutionary and structural data).

Availability: http://insilicogenomics.in/Cry-btIdentifier/welcome.html

Keywords: HTML, PERL, PHP, Access, MySQL, rice, Cry-Bt

Background: Methodology:
Recent advances in molecular biology and genetic engineering help Tool Design and implementation:
scientists to better understand the various mechanisms underlying Cry-Bt identifier was developed and deployed using an open source
plant development and growth. This in turn resulted in development software system. The system used is MySQL database to store gene
of more productive crops possessing resistance to biotic and abiotic and protein sequence data. We used GenBank to retrieve gene
stresses by the introduction of foreign genes. Cry genes from sequence data and the data was processed using a filtering
Bacillus thuringiensis are important sources for development of algorithm. The filtering algorithm was implemented using a set of
insect/pest resistance in plant varieties [1]. Data from increased use routine scripts written in Hypertext Preprocessor (PHP). A
of Cry genes in the development of transgenic plants by scientist GenBank record is considered for retrieving a sequence if the Gene
world wide demands databases and tools for efficient name contains `DNA` or `PROTEIN`. Additionally, the GENE
storage/retrieval of required data. Hence, we describe the record in the FEATURES should also contain terms describing
development of a method to use Cry gene database that enable CRY-BT (for example, ‘Cry1Aa’ or ‘Cry1Ab’ or ‘Cry1Ac’).
identification of Cry genes present in transgenic crops [2-4]. This
will further help in the design of primer sets for the PCR Programs written in PHP enabled database search using keywords
identification of specific Cry genes. The tool also enables users to like `organism name`, `Gene name`, `Gene Id.` and `Gene & Protein
access information related to Cry genes present in different online Sequences` of Cry-Bt genes. The database facilitates to retrieve
literature, nucleotide/protein sequence databases for sequence results in `Text` or `Table` or `Graphical` formats. Detailed
comparison and analysis [5-7]. The tool is designed based on sequence and literature data can be obtained from the corresponding
relational database model that interacts with different sources of hyperlinks. Relational database schema employed in design of the
information located in various online-databases. tool provides representation of the Cry-bt database system with its
filtering algorithm to store, retrieve data with out redundancy up to
3rd normalization form with no loss of functional information [8-
11].

Figure 1: Front view of Cry-Bt identifier.

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ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 4(5): 182-183 (2009) © 2009 Biomedical Informatics
Bioinformation open access
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Figure 2: Representation of Various features (a, b, c &d) that can be performed using Cry-Bt Identifier

The tool is also embedded with a primer design tool- E-PCR Primer3 is a tool for picking primers from a DNA sequence. The
(Electronic PCR). EPCR employs a computational procedure that Biology WorkBench is a web-based tool for biologists. The
identifies sequence tagged sites (STS), present in the user fed DNA WorkBench allows biologists to search many popular protein and
sequences. E-PCR initially looks for potential STS sites present in nucleic acid sequence databases. Database searching is integrated
DNA sequences by searching subsequences that closely match to with access to a wide variety of analysis and modeling tools. Thus,
the PCR primers with correct order, orientation, and spacing that are the developed Cry-Bt identifier database will enable to provide
used to generate known Sequence Tagged Sites. useful information to users.

Embedded E-PCR enables a choice of three options: (1) References:

Identification of suitable restriction enzymes suitable for the given [1] HC Sharma, KK Sharma, Innovations in production,
sequence. (2) Designing a Primer where at the starting positions are biotechnology, quality, and marketing, pages 53 (2006)
placed restriction sites for amplification. (3) Designing a common [2] S Tounsi et al., Biotechnol Lett. 21: 771 (1999) [PMID:]
primer for two genome sequences for a given restriction enzyme. [3] PA Kumar et al., Advances in Applied Microbiology 42:1
This feature enables to find out the best restriction enzyme for the (1996) [PMID: 8865583]
both the homologous sequences. Designing a common primer can [4] R Bhalla et al., FEMS Microbiology Letters 243: 467 (2005)
significantly cut the expenditure on primer design. Here we [5] GT Vilas-Bôas, MV Franco Lemos, Can J Microbiol/Rev can
included information here about online linkage with our Cry-bt microbiol. 50: 605 (2004)
identifier tool to perform in bioinformatical research work. Pfam is [6] FC Chen et al., Biotechnology Letters, 247 (2006) [PMID:]
a large collection of multiple sequence alignments and hidden [7] CM Beron et al., Appl Environ Microbiol. 71:761 (2005)
Markov models covering many common protein domains and [PMID:]
families, ProDom is a comprehensive set of protein domain families [8] Y Mohamed, et al., CIDR. 196-206 (2007)
automatically generated from the SWISS-PROT and TrEMBL [9] J Scaria et al., Bioinformation 1: 5 (2005) [PMID:000000]
sequence databases, helps to discover motifs (highly conserved [10] F Rong et al., Bioinformation 1: 16 (2005) [PMID:000000]
regions) in groups of related DNA or protein sequences using [11] J Dai et al., Bioinformation 1: 214 (2006) [PMID:0000000]
MEME and, search sequence databases using motifs using MAST.
Edited by P. Kangueane
Citation: Singh et al., Bioinformation 4(5): 182-183 (2009)
License statement: This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-
commercial purposes, provided the original author and source are credited.

183
ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 4(5): 182-183 (2009) © 2009 Biomedical Informatics