title: FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.
abstract: BACKGROUND
  Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets.
  
  
  RESULTS
  Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines.
  
  
  CONCLUSIONS
  FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.
authors.affiliation: Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.|Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
authors.forename: Jiwoong
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.|Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
authors.forename: Min Soo
authors.initials: MS
authors.lastname: Kim
authors.affiliation: Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.|Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.|Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
authors.forename: Andrew Y
authors.initials: AY
authors.lastname: Koh
authors.affiliation: Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA. Yang.Xie@utsouthwestern.edu.|Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA. Yang.Xie@utsouthwestern.edu.|Department of Bioinformatics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA. Yang.Xie@utsouthwestern.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA. Xiaowei.Zhan@utsouthwestern.edu.|Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA. Xiaowei.Zhan@utsouthwestern.edu.
authors.forename: Xiaowei
authors.identifier: http://orcid.org/0000-0002-6249-7193
authors.initials: X
authors.lastname: Zhan
mesh_terms: D001419:Bacteria / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003424:Crohn Disease / Q000235:genetics* / Q000382:microbiology; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome / Q000235:genetics*