High-throughput gene discovery in the rat

The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3′ ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to ∼50,000 rat UniGene clusters. We have identified, arrayed, and derived 5′ ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI

Gene transcript clustering: a comparison of parallel approaches Abstract

One of the fundamental components of large-scale gene discovery projects is that of clustering of expressed sequence tags (ESTs) from complementary DNA (cDNA) clone libraries. Clustering is used to create non-redundant catalogs and indices of these sequences. In particular, clustering of ESTs is frequently used to estimate the number of genes derived from cDNAbased gene discovery efforts. This paper presents a novel parallel extension to an EST clustering program,UIcluster4, that incorporates alternative splicing information and a new parallelization strategy. The results are compared to other parallelized EST clustering systems in terms of overall processing time and in accuracy of the resulting clustering. © 2004 Published by Elsevier B.V

ExScal: Elements of an Extreme Scale Wireless Sensor Network

Project ExScal (for Extreme Scale) fielded a 1000+ node wireless sensor network and a 200+ node peer-to-peer ad hoc network of 802.11 devices in a 1.3km by 300m remote area in Florida, USA during December 2004. In comparison with previous deployments, the ExScal application is relatively complex and its networks are the largest ones of either type fielded to date. In this paper, we overview the key requirements of ExScal, the corresponding design of the hardware/software platform and application, and some results of our experiments