Gene machine© - a hardware/software platform for analyzing genome data

Abstract

Gene Machine© is a reconfigurable hardware/software architecture which can be used in studying a variety of problems in the field of computational biology. The key architectural features of Gene Machine© are a) hardware implementation of nth order left-to-right Markov Model where the user ca n specify the number of states of the model and the order of the Markov model; b) cache memory for data input/output; c) shift, and logical instructions which operate at the singleton or set level, and d) floating point and integer arithmetic operations, and variable length operands whose lengths are based on the semantics of the input data. Gene Machine© can be programmed to perform a diverse set of computations such as nucleotide and protein sequence comparisons, pair wise and multiple sequence alignments, and secondary and tertiary structure predictions for DNA, RNA and protein sequences. © Springer-Verlag Berlin Heidelberg 2008.