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Biocomputing Tools and Resources
The revolution in biological sciences has been accompanied by equally dramatic developments in computing hardware and software, with a synergy forming between the large datasets created by laboratories and the tools used to create and analyze them. UCSC offers a rich array of computational facilities and software tools designed for genomic analyses. Most of these resources were developed at the Jack Baskin School of Engineering. Others represent collaborative efforts involving scientists from the Division of Physical and Biological Sciences and the School of Engineering.
Computing Clusters
Two large parallel processor clusters and a bank of web servers support the UCSC Genome Browser and its associated tools and databases. These facilities also support much of the computational genome research conducted at UCSC. The newest of the two clusters, the PitaKluster, consists of 198 dual AMD Opteron processor compute nodes, each having 4 gigabytes of memory, housed in 3 Rackable storage units. The PitaKluster's 396 processors, which run on a Linux operating system, can perform over a trillion instructions/second.
These computing systems are funded through the Howard Hughes Medical Institute, the National Human Genome Research Institute (NHGRI), the California Institute for Quantitative Biomedical Research (QB3), and the National Cancer Institute.
The UCSC Genome Browser
The UCSC Genome Browser provides interactive exploration of metazoan genome sequences. It fuses multiple kinds of genome-wide annotation in a web-based "genome microscope." The genomes are annotated based on high-throughput experimental projects, bioinformatics, and large human-curated data sets. The UCSC Genome Browser allows cross-species comparisons and now features a growing set of images showing expression patterns at both the tissue and cellular levels.
Parasol
Aligning whole genomes against each other is one of the most compute-intensive problems in bioinformatics. By breaking genomes into pieces and distributing smaller jobs to many CPUs, processing time is greatly reduced. Unfortunately, this sometimes results in hundreds of thousands of jobs being queued for processing, and traditional schedulers cannot handle such large queues effectively. Parasol was designed by Jim Kent (UCSC Genome Bioinformatics Group) to schedule extremely large batches of jobs for processing, and responds rapidly to inevitable systems failures that occur on such large clusters by automatically removing a machine from service when a problem is detected. Although originally written for the Kilokluster, Parasol is portable to other operating systems. Parasol is an open source project and available without restriction (credit to the author is required).
BLAT (Blast-like Alignment Tool)
BLAT was designed by Jim Kent for the Genome Browser Database to enable rapid sequence alignments. It can be run directly on the Kilokluster or via the Genome Browser. BLAT is more accurate and 500 times faster than popular tools for DNA sequence alignments, and 50 times faster for protein alignments when comparing vertebrate sequences.
Splicing Microarray Database
The UCSC microarray database enables researchers to store and browse their data via a web interface. This database focuses on representing alternatively spliced forms of mRNAs and data about their expression as detected in DNA microarray experiments. It integrates experimental data obtained from functional genomics research with information about gene structure that is stored in genomic databases
The Improbizer
The Improbizer is a software tool for detecting regulatory motifs in DNA or RNA sequences. It uses a variation of the expectation maximization (EM) algorithm. This tool finds sequence patterns that occur more frequently than those that appear by chance (i.e. background levels). An assortment of hidden Markov models can be used to adjust for the varying nucleotide background and foreground levels of different species. Designed by Jim Kent for the SOE computing clusters, the program is also downloadable.
Protein Structure Prediction Webserver (SAM-T06)
SAM-T02 is a web-based tool for predicting the fold and secondary structure of a target protein sequence. It uses multi-track hidden Markov models and neural nets trained on multiple alignments generated by the SAM-T2K iterated search procedure. SAM was developed by the research groups of Kevin Karplus and Richard Hughey and is maintained at the SOE Center for Biomolecular Science and Engineering. The SAM webserver includes links to download stand-alone programs, which are free to academics, government laboratories, and non-profits.
The Yeast Intron Database
The Yeast Intron Database is a web-based tool with genome level information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Developed by the research groups of Professors Manual Ares (Dept. of MCD Biology) and David Haussler (Dept. of Biomolecular Engineering), the database lists known spliceosomal introns of yeast and documents the splice sites used by this organism. This information is used to understand splicing patterns, how they are regulated globally, and change during evolution. The website also contains graphs, histograms, images, and hidden Markov model information. Data can be both downloaded and submitted on-line.
The Intronerator
The Intronerator is a collection of web-based tools for exploring the molecular biology and genomics of C. elegans, with a special emphasis on alternative splicing. Developed at the Department of MCD Biology by Professor Al Zahler and Jim Kent (now in the Genome Bioinformatics Group), it includes a catalog of alternatively spliced genes, an intron database, software for genome alignment comparisons between species, and many other useful tools for molecular biology studies. |
