title: Metaphor: finding bi-directional best hit homology relationships in (meta)genomic datasets.
abstract: 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.
authors.affiliation: Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Bernd E
authors.initials: BE
authors.lastname: van der Veen
authors.affiliation: School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Hugh M
authors.initials: HM
authors.lastname: Harris
authors.affiliation: School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Paul W
authors.initials: PW
authors.lastname: O'Toole
authors.affiliation: School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland. Electronic address: m.claesson@ucc.ie.
authors.forename: Marcus J
authors.initials: MJ
authors.lastname: Claesson
mesh_terms: D007778:Lactobacillus / Q000235:genetics*; D054892:Metagenome; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: BLAST; Bi-directional Best Hit; Genomics; Metagenomics; homology