An agile functional analysis of metagenomic data using SUPER-FOCUS

Genivaldo Gueiros Z. Silva, Fabyano A.C. Lopes, Robert A. Edwards

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, “What can the organisms in the sample do?” Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPERFOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS.

Original languageEnglish
Title of host publicationProtein Function Prediction
Subtitle of host publicationMethods and Protocols
EditorsDaisuke Kihara
PublisherHumana Press Inc.
Pages35-44
Number of pages10
ISBN (Electronic)978-1-4939-7015-5, 9781493970155
ISBN (Print)978-1-4939-7013-1, 9781493970131
DOIs
Publication statusPublished - 2017
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1611
ISSN (Print)1064-3745

Keywords

  • Agile tool
  • Bioinformatics
  • Functional profiling
  • Metagenomics
  • SEED
  • Sensitive

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    Silva, G. G. Z., Lopes, F. A. C., & Edwards, R. A. (2017). An agile functional analysis of metagenomic data using SUPER-FOCUS. In D. Kihara (Ed.), Protein Function Prediction: Methods and Protocols (pp. 35-44). (Methods in Molecular Biology; Vol. 1611). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7015-5_4