Metaphor: Finding Bi-directional Best Hit homology relationships in (meta)genomic datasets

• Published in: Genomics (San Diego, Calif.) Vol. 104; no. 6; pp. 459 - 463
• Main Authors: van der Veen, Bernd E., Harris, Hugh M., O´Toole, Paul W., Claesson, Marcus J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2014
• Subjects: Bi-directional Best Hit; BLAST; Genomics; homology; Lactobacillus - genetics; Metagenome; Metagenomics; Phylogeny; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software; Metagenomics; Bi-directional Best Hit; homology; BLAST; Genomics
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2014.10.008

As the number of assembled genome and metagenome sequences continue to grow at an ever-increasing pace, so does the need for fast, flexible and automated pipelines for generating meaningful homologous relationships within and between these (meta)genomes. Such relationships, or lack thereof, are crucial for differentiating between microbial organisms and environments at compositional, functional and phylogenetic levels. Metaphor is a standalone application that identifies core genes, unique genes, orthologs and paralogs in complex genomic datasets. It is not only limited to isolate genomes, but can also be applied to metagenomes due to its flexible implementation of Bi-directional Best Hit analysis. Thus, Metaphor can be used for a variety of functional and phylogenetic applications on a multitude of (meta)genome datasets. •There is a need for flexible & automated pipelines finding homologous relationships.•Metaphor quickly finds orthologs, paralogs, core and unique genes.•Uniquely, Metaphor can be applied to both genomes and metagenomes.•Metaphor can be used for a variety of functional and phylogenetic applications.