To identify strain-specific genes (singletons) we used the software tool EDGAR [ 40], whose comparison model is based on pairwise comparisons of protein sequences using blastp [ 41].
This imbalance is particularly problematic in methods based on pairwise associations between proteins, where the expected number of protein pairs sharing functional relationships is an even smaller fraction of all possible protein combinations.
First, based on pairwise sequence comparisons and protein threading results, the sequences from Oculina and Tachypleus are highly similar.
For about two decades, knowledge-based potentials based on pairwise distances – so-called "potentials of mean force" (PMFs) – have been center stage in the prediction and design of protein structure and the simulation of protein folding.
Methods of the third category, which are in the focus of this project, are based on pairwise comparisons of full-length protein sequences and typically involve the use of clustering techniques [19], [20].
However, based on pairwise assays [ 38], GSQUA proteins seem unlikely to function as interaction mediators in Gerbera, since their interaction capacity appears to be limited [ 38].
In contrast, TRIBES and OFAM use the Markov Cluster (MCL) algorithm for protein family assignment based on pairwise similarities [ 27].
CLANS is a Java tool to visualize and analyze protein sequence similarity based on pairwise similarity (BLAST) and well suited for the analysis of large sets of sequences.
It is a clustering tool designed especially to cluster protein or DNA sequences based on pairwise matches returned by the BLAST algorithm.
In protein similarity networks, proteins are represented as points and similarity relationships (based on pairwise structure or sequence alignments that are better than a threshold) are represented as edges connecting the points.
