Chad A. Roberts

ESTprep: preprocessing cDNA sequence reads

MOTIVATION High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Three Complementary Approaches to Parallelization of Local BLAST Service on Workstation Clusters

This paper describes approaches to improving the perfor- mance of one of the most common and increasingly important aspects of the Human Genome Project (HGP) — large-volume, batch comparison of DNA sequence data. This basic comparison operation, usually carried out by the well-known BLAST program on one subject sequence against the internationally-available databases of over 3 million target sequences, is already used hundreds of thousands of times each day by researchers around the world. At present, it is still used primarily in single query, or small batch query mode. As the entire sequence of the human genome nears completion, the area of functional genomics, and the use of micro- arrays of sets of genes, is coming to the fore. These developments will demand ever more efficient means of BLASTing sets of data that will make single processor implementation on powerful workstations infea- sible. We describe the three primary parallel components to BLAST. The first is at the sequence-to-sequence comparison level. The second parallelizes a single query across a partitioned and distributed database. And finally, the set of queries themselves are partitioned across a set of servers with replicated or partitioned databases. The three methods may be employed alone or in concert. Our current implementation is described which parallelizes batch requests, and our plans for implementation of the other levels is also described. The results will ultimately be applied to hardware assistance for this soon-to-be primitive computer operation.

Pooled library tissue tags for EST-based gene discovery

MOTIVATION In gene discovery projects based on EST sequencing, effective post-sequencing identification methods are important in determining tissue sources of ESTs within pooled cDNA libraries. In the past, such identification efforts have been characterized by higher than necessary failure rates due to the presence of errors within the subsequence containing the oligo tag intended to define the tissue source for each EST. RESULTS A large-scale EST-based gene discovery program at The University of Iowa has led to the creation of a unique software method named UITagCreator usable in the creation of large sets of synthetic tissue identification tags. The identification tags provide error detection and correction capability and, in conjunction with automated annotation software, result in a substantial improvement in the accurate identification of the tissue source in the presence of sequencing and base-calling errors. These identification rates are favorable, relative to past paradigms. AVAILABILITY The UITagCreator source code and installation instructions, along with detection software usable in concert with created tag sets, is freely available at http://genome.uiowa.edu/pubsoft/software.html CONTACT tomc@eng.uiowa.edu

A rat heart UniGene set for identification of spatially and/or temporally regulated genes during heart development

A rat heart UniGene set for identification of spatially and/or temporally regulated genes during heart development