Adam Cannane

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Homology search is a key tool for understanding the role, structure, and biochemical function of genomic sequences. The most popular technique for rapid homology search is blast, which has been in widespread use within universities, research centers, and commercial enterprises since the early 1990s. In this paper, we propose a new step in the blast(More)
BLAST is the most popular bioinformatics tool and is used to run millions of queries each day. However, evaluating such queries is slow, taking typically minutes on modern workstations. Therefore, continuing evolution of BLAST--by improving its algorithms and optimizations--is essential to improve search times in the face of exponentially increasing(More)
Search engines are an essential tool for modern life. We use them to discover new information on diverse topics and to locate a wide range of resources. The search process in all practical search engines is supported by an inverted index structure that stores all search terms and their locations within the searchable document collection. Inverted indexes(More)
Compression of large collections can lead to improvements in retrieval times by offsetting the CPU decompression costs with the cost of seeking and retrieving data from disk. We propose a semistatic phrase-based approach called xray that builds a model offline using sample training data extracted from a collection, and then compresses the entire collection(More)
RMIT University participated in two tracks at TREC 2004: Terabyte and Genomics, both for the first time. This paper describes the techniques we applied and our experiments in both tracks, and discusses the results of the genomics track runs; the terabyte track results are unavailable at the time of manuscript submission. We also describe our new zettair(More)
Current adaptive compression schemes such as gzip and compress are impractical for database compression as they do not allow random-access to individual records. The sequitur scheme of Nevill-Manning and Witten also adaptively compresses data, achieving excellent compression but with signiicant main-memory requirements. A preliminary version of sequitur(More)
Fast and accurate techniques for searching large genomic text collections are becoming increasingly important. While Information Retrieval is well-established for general-purpose text retrieval tasks, less is known about retrieval techniques for genomic text data. In this paper, we investigate and propose general-purpose search techniques for genomic text.(More)