Biomedical subjects

Adam Cannane

Publications and source records attributed to Adam Cannane.

3 recordsLinked to original sources

PubMed2006

A deterministic finite automaton for faster protein hit detection in BLAST.

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 collection sizes. We present an optimization to the first stage of the BLAST algorithm specifically designed for protein search. It produces the same results as NCBI-BLAST but in around 59% of the time on Intel-based platforms; we also present results for other popular architectures. Overall, this is a saving of around 15% of the total typical BLAST search time. Our approach uses a deterministic finite automaton (DFA), inspired by the original scheme used in the 1990 BLAST algorithm. The techniques are optimized for modern hardware, making careful use of cache-conscious approaches to improve speed. Our optimized DFA approach has been integrated into a new version of BLAST that is freely available for download at http://www.fsa-blast.org/.

Algorithms↗

PubMed2004

General-purpose search techniques for genomic text.

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. In particular, we show that significant improvements can result from manual term expansion, where additional words are added to queries and documents. We also show that collection partitioning, where documents are included in or excluded from the search space, is highly effective for some tasks. We experiment with our techniques on four text collections and show, for example, that the collection partitioning scheme can improve effectiveness by almost 9.5% over a standard retrieval baseline. We conclude by recommending techniques that can be considered for most genomic search tasks.

Database Management Systems↗

PubMedDate not supplied

Improved gapped alignment in BLAST.

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 algorithm to reduce the computational cost of searching with negligible effect on accuracy. This new step-semigapped alignment-compromises between the efficiency of ungapped alignment and the accuracy of gapped alignment, allowing BLAST to accurately filter sequences with lower computational cost. In addition, we propose a heuristic-restricted insertion alignment-that avoids unlikely evolutionary paths with the aim of reducing gapped alignment cost with negligible effect on accuracy. Together, after including an optimization of the local alignment recursion, our two techniques more than double the speed of the gapped alignment stages in BLAST. We conclude that our techniques are an important improvement to the BLAST algorithm. Source code for the alignment algorithms is available for download at http://www.bsg.rmit.edu.au/iga/.

Algorithms↗