A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences.

ABSTRACT: Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifyi

SUBMITTER: Norrevang AF 

PROVIDER: S-EPMC10763278 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature