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| PROJECTS & DATABASES |
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Quick Link : Solanace Project, Plant Gene Indices, EST Anlaysis for Panning Gene, Expression Databases, Crop Functional Genomics
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| SOLANACEAE PROJECT |
 Korea Tomato Sequencing Project (chormosome 2) sol.kribb.re.kr/tomatogenome/
Tomato Chromose 2 browsing, predicted gene struncture and annotation.The currently displayed annotations generated at KRIBB are preliminary.
The annotations are exclusively derived from alignments of transcript sequences, and gene predictionprograms(FGENESH, GENSCAN, GenSeqer)
have been included.
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Solanaceae Gene Indices sol.pdrc.re.kr
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All publicly available EST, other sequences from GenBank and KRIBB have been assembled into contigs and built into Gene Indices.
Currently Gene Indices have been constructed for six Solanaceae species: Solanum tuberosum (potato), Lycopersicon esculentum (tomato),
Capsicum annuum (pepper), Nicotiana tabaccum (tobacco), Nicotiana benthamiana and Solanum melongena(eggplant).
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International Solanaceae Genomics Project (SOL) sgn.cornell.edu
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Systems Approach to Diversity and Adaptation
Over the coming decade the International Solanaceae Genome Project (SOL) will create a coordianted network of knowledge about
the Solanaceae family aimed at answering two of the most important questions about life and agriculture:
- How can a common set of genes/proteins give rise to such
a wide range of morphologically and ecologically distinct organisms that occupy our planet?
- How can a deeper understanding of the genetic basis of diversity be harnessed to better meet
the needs of society in an environmentally-friendly way?
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Plant Gene Indices
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Solanaceae Gene Indices Gene Indices
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MPEAS Medicinal Plant EST Analysis System
species : Panax ginseng, Allium victorialis, Artemisia princeps, Physaliastrum japonicum,
Capsicum annuum, Nicotiana benthamiana, Ipomoea batatas, Sesamum indicum
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Gene Indices are built using:
ESTScan[ Iseli, C. Jongeneel, C.V., and Bucher, P. (1999) ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions
in EST sequences ISMB 7: 138-148. ]
stackPACKTMTM is an EST clustering system designed by the South African National Bioinformatics Institute and egenetics.
R statistic (Stekel, Git, and Falciani (2000) The comparison of gene expression from multiple cDNA libraries. Genome Research 10:2055-2061).
BLAST Programs Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
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| Panax ginseng EST Analysis |
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| Alternative-Splicing Variants |
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Hot Pepper MicroArray Database plant.pdrc.re.kr/array
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Herbal Medicine MicroArray Database herval.pdrc.re.kr
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Quintet
An open source microarray data analysis System with GUI: Quintet. We address Quintet,
an R-based unified cDNA microarray data analysis system with GUI.
Five principal categories of microarray data analysis have been coherently integrated in Quintet.
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| Crop Functional Genomics |
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Arabidopsis
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Oryza sativa(rice)
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Glycine max(soybean)
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Report
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| EST analysis & functional catalog |
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The gene analysis based on ESTs involves clustering and assembly of EST sequences, chromosomal mapping of consensus sequences obtained from clustering and assembly, and finally gene annotation process. For the EST clustering process, we used StackPACK software from SANBI to make virtual mRNA candidate with high coverage and high quality. To analyze these sequence data further, these process are needed as follow. homology search of consensus sequences using BLASTX against NCBI NR database, protein function categorization according to MIPS (Munich Information center for Protein Sequences) and GO (Gene Ontology) catalog, chromosomal mapping using sim4 tool and the upsteam sequence analysis obtained from genomic mapping. We applied the public softwares such as Gibbs Sampling, MEME (Multiple EM for Motif Elicitation), and TRANSFAC to our research for promoter analysis.
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| DNA chip analysis |
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In the case of clustering analysis of microarray study, validation is one of important data processing step. The notion is generally accepted that co-expressed genes are under the same transcriptional control and are probably categorized into same or similar functional group biologically or biochemically. Thus, the efforts to find common regulatory motifs in their promoter region, or functional grouping the genes in the same cluster are common process for the interpretation and validation of microarray data.
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| Peptide mass fingerprining |
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Public protein sequence database such as SWISS-PROT is used practically for the protein identification from the result of Matrix- Assisted Laser Desorption Ionization-Time OfF light (MALDI-TOF)data, which is one of popular proteomic studies. Howerver, for the less of protein information for the specific plant species in these databases it is needed to construct the private protein database containing sufficient protein information for interpreting massive PMF results about each specific plant species. Thus we tried to make the protein database by translating enormous coding region sequences obtained from EST analysis and the PMF software working on these databases. Therefore, in this study, we tried to make the individual systems about EST based data analysis, regulatory motif information from chromosomal mapping of ESTs, microarray data and PMF information from bench works at first and finally integrate these individual information modules as a whole. That is, we constructed the web-based integrated systems in which the results from gene analysis, microarray analysis, and proteomic analysis are reciprocally connected and complemented with each other.
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| Copyright (c) 2007, Gene plant genomics information. Hosted at KRIBB
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