Which database examples are crucial reference maps for classifying sequenced fragments?
Answer
Greengenes, SILVA, or RDP
The process of taking raw sequenced DNA fragments and assigning them a tentative taxonomic name relies heavily on established reference databases. These databases contain sequences from known microbial genomes and serve as the backbone against which new reads are compared. Key examples of these foundational and continuously curated reference maps include Greengenes, SILVA, and RDP. The quality, maintenance, and specific version of the database used in the analysis pipeline directly impacts the reliability of the resulting taxonomy assignments.
#Videos
Microbiome Labs History - YouTube
Related Questions
What marker gene sequencing enabled the initial analysis of bacterial identification?What early method was used to assign taxa by clustering sequences in initial analysis?What are the two key diversity metrics established by foundational sequencing tools?What technique required entirely new toolsets for assembly and functional analysis?Which foundational tool standardized initial steps for processing 16S data?Who primarily comprised the collection of inventors of microbiome analysis tools?Which database examples are crucial reference maps for classifying sequenced fragments?What did the shift from black-box solutions trend towards in evolving analysis platforms?Why might older papers report very different diversity figures than contemporary ones using the same raw data?What specific diligence should a researcher perform regarding taxonomy assignment validation?