Call for Paper - November 2018 Edition
IJCA solicits original research papers for the November 2018 Edition. Last date of manuscript submission is October 22, 2018. Read More

Biogen Base - An interactive maize database for phenomics platform

Print
PDF
Computational Science - New Dimensions & Perspectives
© 2011 by IJCA Journal
Number 2 - Article 3
Year of Publication: 2011
Authors:
Murukarthick. J.
Senthil. N
Raveendran. M

Murukarthick. J., Senthil. N and Raveendran. M. Biogen Base - An Interactive Maize Database for Phenomics Platform. IJCA Special Issue on Computational Science - New Dimensions & Perspectives (2):56–61, 2011. Full text available. BibTeX

@article{key:article,
	author = {Murukarthick. J. and Senthil. N and Raveendran. M},
	title = {Biogen Base - An Interactive Maize Database for Phenomics Platform},
	journal = {IJCA Special Issue on Computational Science - New Dimensions & Perspectives},
	year = {2011},
	number = {2},
	pages = {56--61},
	note = {Full text available}
}

Abstract

Biogen base serves the maize (Zea mays L.) research community by making a wealth of genetics and genomics data available through an intuitive Web-based interface. We have developed an Open access database as a resource to enhance research with the unique data obtained from the genomics and proteomics lab of TNAU. Biogen Base is an interactive database in bringing out the different traits of the inbreds of Tamil Nadu Agricultural University (UMI - University Maize Inbreds’s) and the SSR Markers. The database interface is developed in PHP and HTML as the front end and MySQL as the backend tools. The webpage was developed using Dreamweaver and the database in MySQL is connected with the web server. The Current version of this database has four major parts and functions; (1) Germplasm - contains 101 germplasm lines and its 28 corresponding traits with values, (2) Genotype Search – enables the search among 31 SSR markers along with the chromosome number, gel patterns, forward and reverse primer, and allele size, (3) Phenotype Search - which contains text descriptions of all the phenotypic terminologies and their corresponding abbreviations stored in the database and (4) Mutant Phenotype Search – contains 5 mutant phenotypes with its traits and values. In addition, it includes brief description about the terms, and links to other publicly available databases. Images of plants with novel characteristics are also available at the web site. The large and growing body of experimental data on maize germplasm and DNA markers is of enormous value in the Genomics and Proteomics laboratories. The database can be searched using a user friendly web interface. This database is publicly available at http://www.tnaugenomics.com/database/maize. It also facilitates the deposition of new values for processing and inclusion in the database to fulfill the priceless work going on in Genomics and Proteomics Laboratory of TNAU.

Reference

  • T.Z. Sen, C.M. Andorf, M.L. Schaeffer, L.C. Harper, M.E. Sparks, J. Duvick, V.P. Brendel, E. Cannon, D.A. Campbell and C.J. Lawrence. MaizeGDB becomes ‘Sequence-cenric’. 2010.
  • M.C. Costanzo, M.S. Skrzypek, R. Nash, E. Wong, G. Binkley, S.R. Engel, B. Hitz, E.L. Hong and J.M. Cherry. The Saccharomyces Genome Database Project. New mutant phenotype data curation system in the Saccharomyces Genome Database. 2009.
  • N. Junjian, P. Anuradha, K. Youens-Clark, Immanuel, Y., Pankaj, J., Isaak, T., Chih, W.T., Liya, R., William, S., Xuehong, W., Shuly, A., Doreen, W., Lincoln, S. and Susan, M. Gramene QTL Database: Development, content and applications. 2009.
  • S. Hunter, R. Apweiler, T.K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, D. Das, L. Daugherty, and Duquenne, L. InterPro: The integrative protein signature database. Nucleic Acids Res., 2009. D211 – D215.
  • H. Mcwilliam, F. Valentin, M. Goujon, W. Li, M. Narayanasamy, J. Martin, T. Miyar and R. Lopez. European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Web services at the European Bioinformatics Institute. 2009.
  • L. Wissler, E. Dattolo, A.D. Moore, T.B.H. Reusch, J.L. Olsen, M. Migliaccio, E. Bornberg-Bauer and G. Procaccini, Dr. Zompo. An online data repository for Zostera marina and Posidonia oceanic ESTs. 2009.
  • K. McLeod and A. Burger, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK. Towards the use of argumentation in bioinformatics: A gene expression case study. 2007.
  • Co te’, R.G., Jones, P., Martens, L., Kerrien, S., Reisinger, F., Lin, Q., Leinonen, R., Apweiler, R. and Hermjakob, H. The Protein Identifier Cross-referencing (PICR) service: Recounciling protein identifiers across multiple source databases. BMC Bioinform, 2007. 8. 401.
  • P. Rice, I. Longden, and Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 2000. 16.
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov and Bourne, P.E. The Protein Data Bank. Nucleic Acids Res., 2000. 28. 235 – 242.
  • R.T. Fielding. Architectural styles and design of network-based software architectures. Ph.D. Thesis. UC Irvine. 2000.