Assignment Generator :: Basic Instructions
Scientists use different methods to identify bacteria such as microscopy and biochemical tests. A different approach uses the sequencing of the 16S rRNA gene. This gene is highly conserved in bacteria (and other organisms) and strongly correlated with their evolutionary history. Therefore, sequencing this gene provides a good idea of the identity of the bacteria without growing and isolating them. This methodology is highly valued and widely used in many scientific fields as diverse as medicine, plant pathology and geochemistry, among others.
1. Download unknown sequence
This file is in fasta format that can be opened with text editors such as TextEdit on Mac OS X and Wordpad on PC. Do not use Notepad on PC to view the file as it will show the string of text on a single line. The format should appear as follows. The first line is devoted to the name of the sequence and always begins with a right caret followed by the name and a carriage return. The sequence begins on the second line and the sequence text soft wraps (no carriage return between lines) until the second and last carriage return of the file signifies the end of the sequence.
>ID "Student name" (carriage return)
SEQUENCE HERE…END (carriage return)
2. Identify close relatives of your sequence and relevant references
- Go to the Ribosomal Database Project at http://rdp.cme.msu.edu
- Go to the Classifier analysis tool.
- Go to "Choose a file to upload" and select your fasta file. Then click on the "Submit" button.
- Record the classification information from Domain to Genus.
3. Find close relatives to sequences
- Go to the Sequence Match analysis tool (also called SEQMATCH).
- Go to "Choose a file to upload" and select your fasta file.
- Change the options below to:
- Strain: Both
- Source: Isolates
- Size: >1200
- Quality: Good
- Taxonomy: Nomenclatural
- KNN matches: 5
- Click on "Submit".
The Sequence Match results show the closest matches and how they fit in the nomenclatural taxonomy.
- Go to "view selectable matches." Only five matches should be displayed. If more than five matches are displayed, go to the bottom of the page and change the options as indicated above.
- Do all the matches have the same classification? If not, record the classification for the matches.
- Change the KNN Matches from 5 to 1. After this, only the closest match will be displayed. Record the name of the closest relative and its S_ab score.
In some cases the name of the sequence will not agree with the classification, that is ok and represents changes in the taxonomy, nomenclature, mislabeling, etc.
Question
What is known about this genus in terms of Ecological importance, usefulness to humans and its potential to cause diseases?
Questions/comments: rdpstaff@msu.edu
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