HMMs have been proven useful in protein sequence analysis. However, a full search of a sequence database using an HMM is computationally expensive. HMMERHEAD is a software package, incorporated into the HMMER [4] HMM suite, that efficiently filters out most of the unrelated sequences while retaining nearly all related ones. A full scan of the NR database [7] takes 767 seconds using HMMERHEAD, w...

Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their variable genome sequences. This study investigates the infection processes in prot...

We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the...

MOTIVATION In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help...

Examination of all against all comparisons (see below) using this scoring function found that some families consistently scored higher than others. For example some families of membrane proteins would score more highly against other membrane proteins probably due to biases in sequence composition. Therefore, for each pairwise comparison of search outputs the following normali-zation is carried ...

We used the Automatic Domain Decomposition Algorithm (ADDA) to generate a database of protein domain families with complete coverage of all protein sequences. Sequences are split into domains and domains are grouped into protein domain families in a completely automated process. The current database contains domains for more than 1.5 million sequences in more than 40,000 domain families. In par...

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...

We have two objectives. First, we want to build a system for detecting tetratricopeptide repeats in protein sequences. Second, we want to demonstrate how the general bioinformatics database integration system called Kleisli can help build such a system easily. We achieve these two objectives by showing that short and clear programs can be written in Kleisli, using its high-level query language ...

The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) is a polyphagous, phytophagous insect that has emerged as a major pest of cotton, alfalfa, fruits, and vegetable crops in the eastern United States and Canada. Using its piercing-sucking mouthparts, TPB employs a "lacerate and flush" feeding strategy in which saliva injected into plant tissue degrades cell wall components and...

Abbreviations: 2D, two-dimensional; BLAST, Basic Local Alignment Search Tool; COG, clusters of orthologous groups; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MOD, Model Organism Database; MS, mass spectrometry; NCBI, National Center for Biotechnological Information; ORF, open reading frame; Pfam, Protein families; PLEX, Protein Link Explorer; TR, transcriptional regulator...