POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence identity across all orthologs shared by two genomes, (ii) genomic fluidity (a measu...

In this paper we first briefly review the literature on similarity relations, and then introduce a dissimilarity relation between a pair of elements in a specific domain. Since in some cases recognizing dissimilarity is easier than similarity, we try to find a connection between these relations based on specific functions.

MOTIVATION A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a co...

In the process of designing pattern recognition systems one may choose a representation based on pairwise dissimilarities between objects. This is especially appealing when a set of discriminative features is difficult to find. Various classification systems have been studied for such a dissimilarity representation: the direct use of the nearest neighbor rule, the postulation of a dissimilarity...

General dissimilarity-based learning approaches have been proposed for dissimilarity data sets [1,2]. They often arise in problems in which direct comparisons of objects are made by computing pairwise distances between images, spectra, graphs or strings. Dissimilarity-based classifiers can also be defined in vector spaces [3]. A large comparative study has not been undertaken so far. This paper...

Case-Based Reasoning is used when generalized knowledge is lacking. The method works on a set of cases formerly processed and stored in the case base. A new case is interpreted based on its similarity to cases in the case base. The closest case with its associated result is selected and presented as output of the system. Recently, Dissimilarity-based Classification has been introduced due to th...