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This tutorial is intended to walk the beginning user through Greengenes. It offers a step by step explanation of how to classify and/or make a tree from the report you received back from a sequencing lab. Below is a table of the necessary steps listing the file types you need to start each step and what files you can expect to receive back from Greengenes. In most cases the output from one step becomes the input for the next step. Vocabulary, acronyms and file types are explained along the way to assist users who may be unfamiliar with them. As well, there are links to background information about different concepts covered by the Greengenes technology.
To begin: You received either a chromatogram or a FASTA file back from the sequencing lab. This is what you need to get started. If you received a chromatogram you will need to start first by base calling (and assembling) your chromatogram. If you received a FASTA file you can skip the base calling step and move along to aligning your report.

Steps in Using Greengenes	Chromatogram to nucleotide bases	Aligning Your Sequences	Removing Chimeric Sequences	Classifying Your Sequences	Make a Tree to Display Results
Input	Chromatogram you received from the sequencing lab	FASTA file	Aligned FASTA file	Non-Chimeric FASTA file	Non-Chimeric FASTA file
Output	FASTA file (or PHD file)	FASTA (aligned) file & Excel report	non-chimeric FASTA file & Excel report	Excel Report	Tree
Software Used	FinchTV or Phred/Phrap	NAST (Greengenes)	Bellerophon3 (Greengenes)	Greengenes	MEGA or QAlign2

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What is the 16S rRNA gene?

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