annotation
Methods and Protocols | Novel Systems Biology TechniquesCurated BLAST for GenomesGiven a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without...
Methods and Protocols | Novel Systems Biology TechniquesPaperBLAST: Text Mining Papers for Information about HomologsWith the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about...
Research Article | Host-Microbe BiologyRNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during InfectionDermatophytoses (ringworm, jock itch, athlete’s foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing...