Abstract
HMMer is a commonly used package for biological sequence database searching with profile hidden Markov model (HMMs). It allows researchers to compare HMMs to sequence databases or sequences to HMM databases. However, such searches often take many hours on traditional computer architectures. These runtime requirements are likely to become even more severe due to the rapid growth in size of both sequence and model databases. We present a new reconfigurable architecture to accelerate the two HMMer database search procedures hmmsearch and hmmpfam. It is described how this leads to significant runtime savings on off-the-shelf field-programmable gate arrays (FPGAs).
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