A computational approach that infers protein-protein interactions from genome sequences is proposed in this paper. It is based on our recent observation that protein-protein interactions can be identified by a set of “unusual” protein-profile pairs in experimentally determined protein interactions. A pair of proteinprofiles is considered to be unusual if its occurrence in the given data is stat...

Pfam 30 (16,306 HMMs) provides the PfamA.full.uniprot file that corresponds to UniProt 2016_02 (46,974,580 proteins). This file was used to obtain dPUC2’s observed family pair counts, CODD’s list of certified domain pairs [1], and DAMA’s domain information and observed architectures [2]. We used the HMMER 3.1b2 version of hmmscan to predict domains (this version is required by Pfam 30). We down...

Databases of multiple sequence alignments are a valuable aid to protein sequence classification and analysis. One of the main challenges when constructing such a database is to simultaneously satisfy the conflicting demands of completeness on the one hand and quality of alignment and domain definitions on the other. The latter properties are best dealt with by manual approaches, whereas complet...

The Abi protein family consists of putative membrane-bound metalloproteases. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes (e.g., pln locus from Lactobacillus plantarum and sag locus from Streptococcus pyogenes), whe...

An important question in protein evolution is to what extent proteins may have undergone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolu...

We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 well-characterized domain families with the remaining do...

AtongFnDomain The functional domains shared by the tested pairs in Tong et al experiment. Description Data developed from Tong et. al. buffering experiments. Usage data(AtongFnDomain) Format A list containing 3 items. pairs Dataframe of all the gene pairs and their synthetic lethality status. SharedPfam List of the Pfam domains shared by each pair. The order of this list is the same as the orde...

Resampling algorithms provide an empirical, non-parametric approach to determine the statistical significance of annotations in different experimental settings. ResA(3) (Resampling Analysis of Arbitrary Annotations, short: ResA) is a novel tool to facilitate the analysis of enrichment and regulation of annotations deposited in various online resources such as KEGG, Gene Ontology and Pfam or any...

One approach for facilitating protein function prediction is to classify proteins into functional families. Recent studies on the classification of G-protein coupled receptors and other proteins suggest that a statistical learning method, Support vector machines (SVM), may be potentially useful for protein classification into functional families. In this work, SVM is applied and tested on the c...