title: MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.
abstract: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.
  
  
  METHODS
  MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2.
  
  
  BACKGROUND
  shallam@mail.ubc.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
authors.forename: Kishori M
authors.initials: KM
authors.lastname: Konwar
authors.affiliation: Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and.
authors.forename: Niels W
authors.initials: NW
authors.lastname: Hanson
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
authors.forename: Maya P
authors.initials: MP
authors.lastname: Bhatia
authors.affiliation: Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada.
authors.forename: Dongjae
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada.
authors.forename: Shang-Ju
authors.initials: SJ
authors.lastname: Wu
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
authors.forename: Aria S
authors.initials: AS
authors.lastname: Hahn
authors.affiliation: Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and.
authors.forename: Connor
authors.initials: C
authors.lastname: Morgan-Lang
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
authors.forename: Hiu Kan
authors.initials: HK
authors.lastname: Cheung
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada, Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software