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Faculty Publications

Bioinformatics

Biology, Bioinformatics

Publication Year

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Full-Text Articles in Life Sciences

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. A. Long, Jianjun Hu Jan 2009

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. A. Long, Jianjun Hu

Faculty Publications

Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane ...


Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara Jan 2005

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara

Faculty Publications

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy ...