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Metaphor: finding bi-directional best hit homology relationships in (meta)genomic datasets.

Authors
  • van der Veen, Bernd E
  • Harris, Hugh M
  • O'Toole, Paul W
  • Claesson, Marcus J
Type
Published Article
Journal
Genomics
Publisher
Elsevier
Publication Date
Dec 01, 2014
Volume
104
Issue
6 Pt B
Pages
459–463
Identifiers
DOI: 10.1016/j.ygeno.2014.10.008
PMID: 25449534
Source
Medline
Keywords
License
Unknown

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.

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