Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we desc...

While many control frameworks exist in the literature, there is a lack of a comprehensive framework for clan control. Clan control is generally studied in a broader context as part of a suite of controls. Researchers have examined clan control from a number of different perspectives, but there is a need for a framework that synthesises and extends existing research. To address this gap, this pa...

Gene Ontology, KEGG pathway, Biocarta Pathway, Panther Pathway, and Pfam information were downloaded from their respective sources. For Pfam, Uniprot IDs were mapped to Entrez Gene IDs, thus resulting in all transcripts for a gene being mapped to the same Pfam terms. Chromosomal location was determined by NCBI cytoband assignment, and gene expression signatures were defined as detailed below. T...

Abstract Recent years have seen a dramatic increase in existence results for tdesigns with large t, i.e. t ≥ 5. Designs are now known to exist for several thousand parameter sets, mostly constructed by the method of orbiting under a group. This note is a contribution to the classification of these designs by parameters. We take an abstract look at admissible parameter sets in general. We introd...

Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these database...

It has long been argued that algorithms that find correlated mutations in multiple sequence alignments can be used to find structurally or functionally important residues in proteins. We examined the properties of four different methods for detecting these correlated mutations. On both simple, artificial alignments and real alignments from the Pfam database, we found a surprising lack of agreem...

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. ...

The most highly conserved regions of proteins can be represented as blocks of aligned sequence segments, typically with multiple blocks for a given protein family. The Blocks Database World Wide Web (http://blocks.fhcrc.org) and e-mail (blocks@blocks. fhcrc.org) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments. We describe features for ...

The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and hierarchically into superfamily and subfamily clusters. The cluster set can be searched with a sequence using the SSMAL search tool or a traditional database search tool like BLAST or FASTA. Additionally a ...

SUMMARY There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have implemented a web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. This detailed knowledge relie...