IEEE Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB

IEEE Transactions on Computational Biology and Bioinformatics (TCBB) will move to the OnlinePlus publication model starting with 2015 issues!

From the May/June 2015 Issue

Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate

By Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, and John L. Spouge

Featured article thumbnail imageOver the past few decades, discovery based on sequence homology has become a widely accepted practice. Consequently, comparative accuracy of retrieval algorithms (e.g., BLAST) has been rigorously studied for improvement. Unlike most components of retrieval algorithms, the E-value threshold criterion has yet to be thoroughly investigated. An investigation of the threshold is important as it exclusively dictates which sequences are declared relevant and irrelevant. In this paper, we introduce the false discovery rate (FDR) statistic as a replacement for the uniform threshold criterion in order to improve efficacy in retrieval systems. Using NCBI’s BLAST and PSI-BLAST software packages, we demonstrate the applicability of such a replacement in both non-iterative (BLAST $_{FDR}$) and iterative (PSI-BLAST$_{FDR}$) homology searches. For each application, we performed an evaluation of retrieval efficacy with five different multiple testing methods on a large training database. For each algorithm, we choose the best performing method, Benjamini-Hochberg, as the default statistic. As measured by the threshold average precision, BLAST $_{FDR}$ yielded 14.1 percent better retrieval performance than BLAST on a large (5,161 queries) test database and PSI-BLAST $_{FDR}$ attained 11.8 percent better retrieval performance than PSI-BLAST. The C++ source code specific to BLAST $_{FDR}$ and PSI-BLAST$_{FDR}$ and instructions are available at

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  • TCBB celebrates its 10th Anniversary. Editor-in-Chief Ying Xu says, "The emergence and maturation of increasingly more and powerful molecular measurement technologies such as next generation sequencing and chromosome conformation capture allow scientists to tackle biological problems at the depth and breadth that we have never seen before. At the same time the enormity and complexity of the data generated using these technologies raised tremendous challenges to computational scientists to develop more effective techniques to store, transmit, organize, process, analyze and mine the data, and to construct models to assist interpreting the data. Since its creation ten years ago, TCBB has been playing a major role in bridging the world of computing and the world of biology. I want to congratulate what the journal has done in providing biologists with the most powerful computational tools to help address their data and modeling needs. I fully expect that TCBB will continue to play increasingly significant roles in attracting more computational scientists to address the ever increasing needs for new and more powerful computational techniques and to introduce to new comers the important and challenging computational biology problems in a timely fashion."

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TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.

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