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HMM/NN simulator

A number of projects described in the book Bioinformatics have been carried using the machine learning software environment for biological sequence analysis developed in collaboration by Net-ID, Inc. and employees at the Danish Center for Biological Sequence Analysis.

The foundation for the software environment is based on NetLibs, an object-oriented library of C++ classes for graphical modeling, machine learning, and inference developed by Net-ID. The library supports the hierarchical and recursive implementation of any graphical model (NNs, HMMs, Bayesian Networks, etc.) together with general local message-passing algorithms for the propagation of information, errors, and evidence during inferential/learning processes and dynamic programming.

Net-Libs provides, among other things, the foundation, for an HMM simulator and an NN simulator for biological sequence analysis. The easy-to-use graphical interface for both simulators is in Java. The software environment runs both under Unix and NT platforms.

In addition, the software environment contains facilities for manipulating input/output sequences, databases, and files, as well as libraries of trained models. The libraries include HMMs for a number of protein families and DNA elements (promoters, splice sites, exons, etc.) and a number of NNs for the detection of particular structural or functional signals, both in protein and DNA sequences.

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