Galaxy |

Primer.design (version 1.39.5.0)

fasta - provide aligned fasta file:

list - OTU list file:

label - OTU Labels:

If none selected, the first label in your file will be used

otulabel - choose an OTU name:

name - names file associated with your fasta file:

count - a count table associated with your fasta file:

pdiffs - specify the number of differences allowed in the primer:

length - indicate the length of the primer:

mintm - indicate minimum melting temperature:

maxtm - indicate maximum melting temperature:

cutoff - set a percentage of sequences that support the base:

For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The primer.design allows you to identify sequence fragments that are specific to particular OTUs.