Bioinformatics Research Group

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Bioinformatics Group Software Tools The following software tools have been developed by members of our research group. Protein folding RAPTOR RAPTOR is a protein threading program taking the pairwise contact potentital into account explicitly. The threading problem is formulated into a large scale Integer Program and solved by branch-and-cut method. Support Vector Machines are used to do fold recognition. Product page (BSI) Web server (on our servers) Jinbo Xu, Ming Li, Dongsup Kim, Ying Xu. RAPTOR: Optimal Protein Threading by Linear programming. Journal of Bioinformatics and Computational Biology, 2003. Details Protein sequencing Champs Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy. Website Download Xiaowen Liu, Yonghua Han, Denis Yuen, Bin Ma. Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy. Bioinformatics, 2009. Details Homology search PatternHunter A program for rapid DNA sequence comparison with similar functionality to BLAST (but faster). Product page (BSI) Download for academic use (BSI) Web server (BSI) Bin Ma, John Tromp, Ming Li. PatternHunter: faster and more sensitive homology search. Bioinformatics, 2002. Details Homologous Genes Search A program that, for a given gene structure, finds quickly similar genes in the same or related species. The program can recover missing exons that has been lost in evolution. The program works very well for genomes as distant as human/mouse divergence. Download (java implementation) Gene finding ExonHunter ExonHunter is a comprehensive gene finder based on hidden Markov models allowing use of variety of additional sources of information (ESTs, proteins, genome-genome comparison, repeats, and more). Download (binary for Linux on x86) Requests for features/downloads: Brona Brejova, Daniel G. Brown, Ming Li, Tomas Vinar. ExonHunter: a comprehensive approach to gene finding. Bioinformatics, 2005. ISMB 2005. Details Mikroskop Mikroskop is a flexible tool for creating diagrams of sequence annotations, such as results of gene finding, homology search, EST mapping, etc. It creates diagrams in EPS or PDF formats and it accepts GTF files, simple files containing quantitative infomation, and ExonHunter advisor files. Download Transmembrane protein topology AHMM AHMM is a transmembrane protein topology program. Given a putative transmembrane protein, the program predicts inside, outside and the membrane spanning part of the protein. Based on the assumption that there are functional domains that occur preferentially internal or external to the membrane, we have extended the model of TMHMM, incorporating functional domain information from Prosite into it. Web server Emily Wei Xu, Paul Kearney, Daniel G. Brown. The use of functional domains to improve transmembrane protein topology prediction. Journal of Bioinformatics and Computational Biology, 2006. Details Applications of bioinformatics methods SID - Plagiarism Detection Tool SID stands for Shared Information Distance or Software Integrity Detection. It detects similarity between programs by computing the shared information between them. It was originally an algorithm developed for comparing how similar or dissimilar genomes are. It was then realized that this algorithm could be extended to many other applications including finding chain letter history and detecting plagiarism. Web server Xin Chen, Brent Francia, Ming Li, Brian Mckinnon, Amit Seker. Shared Information and Program Plagiarism Detection. IEEE Transactions on Information Theory, 2004. Details Phylogenetic analysis PhyloSample PhyloSample is a software package which can generate uniform random taxon samples from a given phylogenetic tree based on different constraints (constrained depth, edge length, or pairwise distance). Web server Download Paul Kearney, Ian Munro, Derek Phillips. Efficient Generation of Uniform Samples from Phylogenetic Trees. In Algorithms and Bioinformatics: 3rd International Workshop (WABI), 2003. Details Expression arrays TreeArrage and Treeps A program for reordering and displaying expression array data. Download Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Alejandro Lopez-Ortiz, Tomas Vinar. Finding Hidden Independent Sets in Interval Graphs. Technical Report CS-2001-26, University of Waterloo, December 2001. Details DNA compression GenCompress/GenDistance GenCompress is an efficient compression algorithm for DNA sequences. Recently, data compression became a tool to retrieve information hidden in genetic sequences. From GenCompress results a shared information distance value is approximately calculated, which measures the relatedness between each pair of DNA sequences. Shared information distance is defined in Kolmogorov complexity theory. Download DNACompress DNAcompress is a fast and efficient compression algorithm for DNA sequences. In the spirit of Lempel-Ziv compression scheme, it first finds all approximate repeats that would provide compression profits via PatternHunter, and then encodes each of them by a pointer to its previous occurrence. Download Xin Chen, Sam Kwong, Ming Li. A compression algorithm for DNA sequences based on approximate matching. In Proceedings of the Tenth Workshop on Genome Informatics (GIW), 1999. Details Research tools med2bib Script that downloads records from PubMed database and saves them in BibTeX format to use as references in TeX documents. Download Web server

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