How to Cite
Downloads
Most read articles by the same author(s)
- Luis Fernando Rivera, Carlos Eduardo Orozco, Andrés Chalarca, INFORMATION SYSTEM FOR LHE MANAGEMENT OF MOLECULAR DATA IN COFFEE: L. DEVELOPMENT AND USE OF TOOLS , Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales: Vol. 32 No. 124 (2008)
Métricas Alternativas
Dimensions
Abstract
Cenicafé has carried out the development of a Bioinformatics platform for the storage, analysis and easy accessibility of the data of the project that study the genomes of several coffee species, the coffee berry borer and the fungus Beauveria bassiana. The projects that involve the construction of cDNA libraries and the development of sequences of ESTs have as a common goal to catalogue the genes of a particular species. In the present study we describe the databases developed at Cenicafé and the statistics of the sequences stored until May 2007. These databases include the corresponding analysis of “Trancript Assemblies” from sequences of ESTs, microsatellites molecular markers (SSRs) and BES (BAC-End sequences). The system developed has implemented Web interfaces for the access, easy accessibility and utilization for the scientists in genome projects since the system can be accessed from any computer at Cenicafé through a system of authentication that permits to maintain the data secure. The system developed permits an ample growth and the access to the information brought up to date of each species studied in an efficient and fast way.
Keywords
References
Ewing B, Hillier L, Wendl M, Green P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8:175-185.
Huang X.; Madan A. 1999. CAP3: A DNA Sequence Assembly Program. Genome Research 9: 868-877.
Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Pétiard V, Tanksley SD. 2005. Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. 112: 114-130.
Montoya, G.; Cristancho, M.A.; Moncada M.P. 2006. Análisis de secuencias de genes de Coffea arabica var. Caturra. Cenicafe 57: 79-87.
Pertea G, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush. 2003. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
Samson, N., Michael G. Bausher, Seung-Bum Lee, Robert K. Jansen, Henry Daniell 2007. The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms Plant Biotechnology Journal 5 (2): 339-353.
Smit, AFA, Hubley, R & Green, P. RepeatMasker Open 3.0. 1996-2004 <http://www.repeatmasker.org>.
Teufel, A, Markus Krupp, Arndt Weinmann, Peter R. Galle. 2006. Current bioinformatics tools in genomic biomedical research (Review). International Journal of Molecular Medicine 17: 967-973.
Thiel T, Michalek W, Varshney RK, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
Zhang Z., Schwartz S., Wagner L., & Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7(1-2): 203-214.
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Copyright (c) 2023 Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales