For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a
popular tool for microbial genome annotation and comparative genomics. Initially created for …

As random shotgun metagenomic projects proliferate and become the dominant source of
publicly available sequence data, procedures for the best practices in their execution and …

Next‐generation technologies generate an overwhelming amount of gene sequence data.
Efficient annotation tools are required to make these data amenable to functional genomics …

Abstract The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource
specialized in the enzymes that build and breakdown complex carbohydrates and …

Due to the rapid release of new data from genome sequencing projects, the majority of
protein sequences in public databases have not been experimentally characterized; rather …

DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD)
form a rich source of information for taxonomic and ecological meta-analyses. However …

Comparative genomics is the cornerstone of identification of gene functions. The immense
number of living organisms precludes experimental identification of functions except in a …

Abstract EnTAP (Eukaryotic Non‐Model Transcriptome Annotation Pipeline) was designed
to improve the accuracy, speed, and flexibility of functional gene annotation for de novo …

Molecular data form an important research tool in most branches of mycology. A non-trivial
proportion of the public fungal DNA sequences are, however, compromised in terms of …

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at
http://hamap. expasy. org/) is a system for the automatic classification and annotation of …