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If you have any problems with these programs, please email email@example.com
- Excavator 2.0
- DomainParser 2
- Excavator 1.0
- RDC Prospect
- P-MAP P-MAP server
Or try our bug reporting site
Open Source Projects
Excavator 2.0Excavator 2.0 websiteExcavator is a computer software program for gene expression data clustering. It uses a set of unique clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. Excavator represents data internally as a minimum spanning tree and outputs results to the user through the use of a micro-array data window, graphs, and a dendrogram viewer.
OS Version Complete Archive Source JAR Binary JAR Documentation Linux 1.0 excavator.tar.gz excavatorSource.jar excavatorBinary.jar excavatorDocs.tar.gz Windows 1.0 Coming soon Mac OSX 1.0 Coming soon
Dong Xu | Victor Olman | Jizhu Lu | Dustin Beadle | Ying Xu
Cubic is a tool developed by the Computational Systems Biology Laboratory at the University of Georgia to be used for protein binding site prediction. Cubic was originally developed by Dr. Victor Olman and then was further developed and optimized (upto 10 times speedup on single-CPU machines) by Dr. Jizhu Lu. Cubic accepts up-stream sequences and a few other parameters as input and generates a set of binding sites and their statistical significance as output.
JCUBIC is a Java-based GUI for CUBIC program which can be used for transcription factor binding site prediction.
- Full CUBIC_2.0.2 Package
- CUBIC-2.0.2 Binaries (Linux)
- CUBIC-2.0.2 Source Code
- Full CUBIC_2.0.1 Package
- CUBIC_2.0.1 Binaries (Linux)
- CUBIC_2.0.1 Source Code
- Full CUBIC_2.0 Package
- CUBIC_2.0 Binaries (Linux)
- CUBIC_2.0 Source Code
- JCubic-1.0.tar.gz (as of April 27th, 2005 this fixes a broken post)
Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu. CUBIC: Search for Binding Sites. CSB 2004: 666-667
Victor Olman | Jizhu Lu | Ying Xu
JpopJPOP (Joint Prediction of Operons) program JPOP is a set of java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome:
1) COG (cluster of orthologs) assignments;
2) Phylogenetic profiles of genes;
3) Intergenic distances between gene pairs.
Version 0.1 downloadCitation of the program:Xin Chen, Zhengchang Su, Ying Xu and Tao Jiang. Computational prediction of operons in Synechococcus sp. WH8102. Gemone Informatics 15: 211-222, 2004.
Xin Chen | Zhengchang Su | Ying Xu | Tao Jiang
Closed Source ProjectsBy downloading any of the following packages you agree to use protected software from the Oak Ridge National Labs (ORNL) and the Computational System Biology Lab (CSBL) of University of Georgia Athens, for research purposes only. You will not transfer or redistribute this program to other laboratories. You agree that any public report or publication of results obtained using protected software will acknowledge its use by an appropriate citation.
This licence does not cover or apply to open source software Released by CSBL.
PROSPECTPROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is a threading-based protein structure prediction system. PROSPECT is designed particularly for the recognization of the fold template whose sequence has insignificant homology to the target sequence.
The Online Manual
Prospect The Entire Packageprospect.tar.gz (96 Megs)
Prospect by parts:Prospect bin folder prospect_bin.tar.gz (2 Megs)
Prospect bin for MacosX folderprospect_bin_macosx.tar.gz(4 Megs)
Prospect data folder prospect_data.tar.gz (94 Megs)
If you use PROSPECT, please refer to:Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.D. Kim, D. Xu, J. Guo, K. Ellrott, Ying Xu, "PROSPECT II: protein structure prediction program for genome-scale application", Protein Engineering, 16 (9), 641 - 650, 2003
Dong Xu | Dongsup Kim | Jun-tao Guo | Kyle Ellrott | Ying Xu
DOMAINPARSER2DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact. A two-domain decomposition problem is solved by finding a cut of the network, which minimizes the total cross-edge capacity (minimum cut).
If you use Domainparser2 please refer to:"Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain Decomposition using a Graph-Theoretic Approach." Bioinformatics. 16:1091-1104. 2000.J. Guo, D. Kim,. D Xu, and Ying Xu. "Improving the Performance of DomainParser for Structural Domain Partition using Neural Network", Nucleic Acids Research, 31(3):944-52.
Dong Xu | Jun-tao Guo | Ying Xu
EXCAVATOR 1.0EXCAVATOR is a computer software for gene expression data clustering. It employs a set of unique clustering algorithms developed by the Protein Informatics Group of Oak Ridge National Laboratory.
The Online Manual
Platform Includes Java VM Without Java VM Command line executable PC (Windows) Download (7344K) Download (1492K) Download (120K) Solaris Download (7684K) Download (1312K) Download (72K) Linux Download (7684K) Download (1312K) Download (72K) DEC Alpha Download (7692K) Download (1320K) Download (116K)
Note: The interface packages (including Java VM or without Java VM) contain command line executables.
If you use EXCAVATOR, please refer to:Ying Xu, Victor Olman, and Dong Xu. Clustering Gene Expression Data Using a Graph-Theoretic Approach: An Application of Minimum Spanning Trees. Bioinformatics. In press.D. Xu, V. Olman, L. Wang, and Ying Xu, "EXCAVATOR: a computer program for gene expression data analysis", Nucleic Acids Research, 31(19), 5582-5589, 2003
Dong Xu | Victor Olman | Li Wang | Ying Xu
RDC ProspectRDC-PROSPECT is a computer program for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the 15N-1H RDC data of the protein recorded in a single ordering medium. It uses only RDC data and predicted secondary structure information. Threading is performed against SCOP 40 structure database (currently v1.65, release of Dec, 2003). The alignment and Z-score for the top 20 ranked templates are reported in the output file.
Qu Y, Guo JT, Olman V, Xu Y. (2004) Protein structure prediction using sparse dipolar coupling data. Nucleic Acids Res.,32, 551-561.
Y. Qu, J.-T. Guo, V. Olman, and Y. Xu, Protein Fold Recognition Through Application of Residual Dipolar Coupling Data, Pacific Symposium on Biocomputing, 2004, 459-470.
Youxing Qu | Jun-tao Guo | Victor Olman | Ying Xu
Promocoprint_template_tail("/home/www/html/templates/template.html"); ?>PROMOCO is a tool developed by the Computational Systems Biology Laboratory at the University of Georgia to be used for protein binding site prediction. It includes the graphical user interface, JPromoco.Power Point of Results
- Yeast_seq.tar.gzCollected from SCPD database
- Ecoli_seq.tar.gzCollected from Dr. Peng Wang and Dr. ZhengChang Su and Dr. Phuongan Dam
Jizhu Lu | Guojun Li | Brian Salvati | Victor Olman | Ying Xu