Alan P. Boyle

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MOTIVATION Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data(More)
The complete genomic sequences for many organisms, particularly primitive organisms with relatively small genomes (prokaryotes), are now available. We describe an approach that supports interactive exploration of patterns in genomic data by combining use of positional weight matrices, the k-means clustering algorithm, and a visualization tool. Users(More)
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