Protein domains are the common currency of protein structure and function. Over 10,000 such protein families have now been collected in the Pfam database. Using these data along with animal gene phylogenies from TreeFam allowed us to investigate the gain and loss of protein domains. Most gains and losses of domains occur at protein termini. We show that the nature of changes is similar after sp...

Recently we proposed a novel method of alignment-alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present several examples of the relations between PFAM protein families that were detected by COMPASS and that lead to the predictions of presently unresolved protein structures. We discuss relatively straigh...

Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by...

UNLABELLED We present the development of a Comprehensive database of 12 076 invariant Peptide Signatures (CoPS) derived from 52 bacterial genomes with a minimum occurrence in at least seven organisms. These peptides were observed in functionally similar proteins and are distributed over nearly 1250 different functional proteins. The database provides function, structure and occurrence in bioche...

Cellulolytic enzymes are generally composed of multienzyme systems and are divided into three classes, endoglucanase, exoglucanase and β-glucosidase. They work synergistically to hydrolyze cellulose molecules to glucose. Fungal exoglucanase (CBH) is a unique enzyme, capable of degrading highly ordered crystalline cellulose. Here we report the isolation of both genomic and cDNA clone and coding ...

The accurate prediction of co-evolving pairs in protein sequences plays an important role in tertiary protein structure prediction and protein engineering. Using information theory to detect coevolving pairs is impacted by the phylogenetic effect on entropy measurements. Mutual Information (MI) is used to detect co-evolving pairs in a protein family by re-sampling based on mutation events in th...

Protein family databases are an important resource for protein annotation and understanding protein evolution and function. In recent years hidden Markov models (HMMs) have become one of the key technologies used for detection of members of these families. This paper reviews the Pfam, TIGRFAMs and SMART databases that use the profile-HMMs provided by the HMMER package.

The Diatom EST database provides integrated access to expressed sequence tag (EST) data from two eukaryotic microalgae of the class Bacillariophyceae, Phaeodactylum tricornutum and Thalassiosira pseudonana. The database currently contains sequences of close to 30,000 ESTs organized into PtDB, the P.tricornutum EST database, and TpDB, the T.pseudonana EST database. The EST sequences were cluster...

Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), the brown marmorated stink bug, is an invasive agricultural and nuisance pest rapidly expanding its incidence in North America. This voracious pest poses a significant threat to rural and urban agriculture, especially to specialty crops such as apples, grapes and ornamentals, as well as staple crops including soybean and corn. The object of ...