PfamAlyzer: domain-centric homology search

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

We present 'dcGO' (http://supfam.org/SUPERFAMILY/dcGO), a comprehensive ontology database for protein domains. Domains are often the functional units of proteins, thus instead of associating ontological terms only with full-length proteins, it sometimes makes more sense to associate terms with individual domains. Domain-centric GO, 'dcGO', provides associations between ontological terms and pro...

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins

Annotations of the genes and their products are largely guided by inferring homology. Sequence similarity is the primary measure used for annotation purpose however, the domain content and order were given less importance albeit the fact that domain insertion, deletion, positional changes can bring in functional varieties. Of late, several methods developed quantify domain architecture similari...

Genetic Drifts in PKR-EIF2A Phosphorylation Homology Domain Region in Iranian HCV Positive Patients during Interferon Therapy

Expression analyses of endoglucanase gene in Penicillium oxalicum and Trichoderma viride

The expression of endoglucanase gene and protein profile belonging to two fungal species, Penicillium oxalicum 1SMS and Trichoderma viride 156MS with high cellulase enzyme activity, was investigated. Fungal isolates were cultured on inducer CMC medium and then the amount of released sugar and protein were assayed every three days for a month, using arsenate molybdatereagent and Bradford method,...

Patternhunter Ii: Highly Sensitive and Fast Homology Search

Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.