Previous works have already checked the relationship of a number of functional similarity scores with different types of biological information: sequences, protein families, expression profiles, pathways, literature, etc. This work aims to provide a review and a critical comparison of previously proposed similarity scores, to help in the decision of choosing the appropriate one for the problem ...

The concept of nucleic acid sequence base alternations is presented. The number of base alterations for the sequences of different length is established. The definition of "enlarged similarity" of nucleic acids sequences on the basis of sequence base alterations is introduced. Mutual information between sequences is used as a quantitative measure of enlarged similarity for two compared sequence...

This work proposes a similarity measure between secondary structures of proteins capable of fusing cell membranes and its implementation in a classification system. For the evaluation of the metric we used secondary structures estimated from amino acid sequences of Class I and Class II viral fusogens (VFs), as well as VFs precursor proteins. We evaluated three different classifiers based on k-N...

Understanding genetic structure and status of genetic variation of Fasciola hepatica isolates from different hosts, has important implications on epidemiology and effective control of fasciolosis. Random amplified polymorphic DNA (RAPD-PCR) was used to study the genetic variation of F. hepatica in sheep and cattle. DNA was extracted from adult helminthes removed from livers of each infected ani...

We are developing a [Molecular] Biological Information System (MoBIoS) based on metric space indices. Unfortunately, common similarity measures for sequence alignment do not form a metric-distance function. This is particularly vexing since the usual definition of edit distance does form a metric. Most clearly, the use of PAM log-odds matrices [2] yields higher similarity scores for more closel...

The clustering of biological sequences into biologically meaningful classes denotes two computationally complex challenges: the choice of a biologically pertinent and computable criterion to evaluate the clusters homogenity, and the optimal exploration of the solution space. Here we are analysing the clustering potential of a new method of sequence similarity based on statistical sequence conte...

With the rapid development of biotechnologies, many types of biological data including molecular networks are now available. However, to obtain a more complete understanding of a biological system, the integration of molecular networks with other data, such as molecular sequences, protein domains and gene expression profiles, is needed. A key to the use of networks in biological studies is the ...