FunGene: the functional gene pipeline and repository
Autor: | Jordan A. Fish, Benli eChai, Qiong eWang, Yanni eSun, C. Titus eBrown, James M. Tiedje, James R. Cole |
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Jazyk: | angličtina |
Rok vydání: | 2013 |
Předmět: |
Microbiology (medical)
functional genes lcsh:QR1-502 Computational biology Biology microbial ecology phylogeny amplicon analysis Microbiology lcsh:Microbiology DNA sequencing 03 medical and health sciences amplification primers Methods Article Gene 030304 developmental biology Genetics 0303 health sciences Phylogenetic tree 030306 microbiology biogeochemical cycles 15. Life on land Amplicon Ribosomal RNA 16S ribosomal RNA Horizontal gene transfer Reference genome |
Zdroj: | Frontiers in Microbiology, Vol 4 (2013) Frontiers in Microbiology |
ISSN: | 1664-302X |
DOI: | 10.3389/fmicb.2013.00291 |
Popis: | Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes. |
Databáze: | OpenAIRE |
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