An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space.

ABSTRACT: The deluge of genomic data raises various challenges for computational protein annotation. The definition of superfamilies, based on conserved folds, or of families, showing more recent homology signatures, allow a first categorization of the sequence space. However, for precise functional annotation or the identification of the unexplored parts within a family, a division into subfamilies is essential. As curators of an expert database, the Carbohydrate Active Enzymes database (CAZy), we began, more than 15 years ago, to manually define subfamilies based on phylogeny reconstruction. However, facing the increasing amount of sequence and functional data, we required more scalable and reproducible methods. The recently popularized sequence similarity networks (SSNs), allows to cope with very

SUBMITTER: Hornung BVH 

PROVIDER: S-EPMC10461819 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature