UBViz: a software tool for exploring metabolic pathways in 3-D space.
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Algorithms↗
Biomedical subjects
Hui-Hsien Chou
Publications and source records attributed to Hui-Hsien Chou.
VECT: an automatic visual Perl programming tool for nonprogrammers.
Modern high-throughput biological research produces enormous amount of data that must be processed by computers, but many biologists dealing with these data are not professional programmers. Despite increased awareness of interdisciplinary training in bioinformatics, many biologists still find it difficult to create their own computational solutions. VECT, the Visual Extraction and Conversion Tool, has been developed to assist nonprogrammers to create simple bioinformatics without having to master a programming language. VECT provides a unified graphical user interface for data extraction, data conversion, output composition, and Perl code generation. Programming using VECT is achieved by visually performing the desired data extraction, conversion, and output composition tasks using some sample user data. These tasks are then compiled by VECT into an executable Perl program, which can be saved for later use and can carry out the same computation independently of VECT. VECT is released under the GNU General Public License and is freely available for all major computing platforms including Macintosh OS X, Linux, and Microsoft Windows at www.complex.iastate.edu.
Computational Biology↗
Picky: oligo microarray design for large genomes.
MOTIVATION: Many large genomes are getting sequenced nowadays. Biologists are eager to start microarray analysis taking advantage of all known genes of a species, but existing microarray design tools were very inefficient for large genomes. Also, many existing tools operate in a batch mode that does not assure best designs. RESULTS: Picky is an efficient oligo microarray design tool for large genomes. Picky integrates novel computer science techniques and the best known nearest-neighbor parameters to quickly identify sequence similarities and estimate their hybridization properties. Oligos designed by Picky are computationally optimized to guarantee the best specificity, sensitivity and uniformity under the given design constrains. Picky can be used to design arrays for whole genomes, or for only a subset of genes. The latter can still be screened against a whole genome to attain the same quality as a whole genome array, thereby permitting low budget, pathway-specific experiments to be conducted with large genomes. Picky is the fastest oligo array design tool currently available to the public, requiring only a few hours to process large gene sets from rice, maize or human.
Algorithms↗
LUCY2: an interactive DNA sequence quality trimming and vector removal tool.
UNLABELLED: Lucy2 is a raw DNA sequence trimming and visualization tool based on the popular command-line Lucy1. Users can change parameters, trim multiple sequences and visualize the results within an integrated, easy-to-use graphical user interface. Lucy2 is designed specifically for non-programmers to use, and is currently available on Windows, Linux and MacOS X. Source code is also available for porting to the other platforms. AVAILABILITY: Lucy2 is distributed under the GNU General Public License and can be downloaded from www.complex.iastate.edu
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Efficient combination of multiple word models for improved sequence comparison.
MOTIVATION: Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes. RESULTS: We describe an improved method for finding similar regions between two sets of DNA sequences. The new method generalizes existing methods by locating word matches between sequences under two or more word models and extending word matches into high-scoring segment pairs (HSPs). The method is implemented as a computer program named DDS2. Experimental results show that DDS2 can find more HSPs by using several word models than by using one word model. AVAILABILITY: The DDS2 program is freely available for academic use in binary code form at http://bioinformatics.iastate.edu/aat/align/align.html and in source code form from the corresponding author.
Algorithms↗