OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.

ABSTRACT: Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. For example, a hemoglobin which branched out prior to the hemoglobin alpha/beta duplication could be closest to a hemoglobin alpha or beta sequence, whereas it is neither. To overcome this problem, phylogeny-driven tools have emerged but rely on gene trees, whose inference is computationally expensive. Here, we first show that in multiple animal and plant datase

SUBMITTER: Rossier V 

PROVIDER: S-EPMC8479680 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature