Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data?: Difference between revisions
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'''How do I create OTUs from 16S sequence data?''' | '''How do I create OTUs from 16S sequence data?''' <br> | ||
james robert white, whitej@umd.edu | james robert white, whitej@umd.edu <br> | ||
<br> | |||
To begin: | To begin:<br> | ||
You need a fasta file of 16S sequences. | You need a fasta file of 16S sequences.<br> | ||
1. Make sure all sequences are in the correct orientation. You may need to reverse complement several. | 1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.<br> | ||
2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT. | 2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.<br> | ||
Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP) | Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)<br> | ||
3. Create a distance matrix from your MSA. | 3. Create a distance matrix from your MSA.<br> | ||
<br> | |||
Revision as of 19:58, 6 January 2009
How do I create OTUs from 16S sequence data?
james robert white, whitej@umd.edu
To begin:
You need a fasta file of 16S sequences.
1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.
2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.
Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)
3. Create a distance matrix from your MSA.