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Abstract

Methods for identifying a molecular system that is similar to at least one model molecular system are provided. The methods may comprise a) establishing an inventory including genetic content, genomic organization and at least one discriminating trait for at least one model molecular system; b) determining from the inventory(ies) of step a) a non-redundant list of protein components of the at least one model molecular system; c) associating a protein component profile encoded by a hidden Markov model (HMM) for each non-redundant protein component; d) providing at least one set of protein sequences obtained from genome data corresponding to a contig of an ordered sequence dataset; e) similarity searching the set of protein sequences obtain from genome data with the protein component profiles of c); f) selecting hit proteins that match the searched protein component profiles from among the set of protein sequences obtain from genome data; g) building clusters using hit proteins selected in step f) according to the genomic organization specified for the model molecular system; h) selecting clusters including protein components of a single model molecular system according to the genetic content and discriminating traits specified for the model molecular system; and i) filling inventories of compatible model molecular systems using clusters from step h).

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