Is it possible to search for a specific sequence in a fastq file with mothur?

Commands in mothur
1

Hi guys,
I would like to know if it is possible to search fastaq datasets for a specific sequence used as input. This can be useful to me because in the databases (Silva, GG etc) there are no certain genera of bacteria, such as non-culturable.

Thanks in advance

2

Sorry, but I’m not sure what you’re asking. We do not have a function where you can give it a sequence and it gets compared against a fastq file. Also, “non-culturable” isn’t a genus; however, “unclassified” might appear as a genus for many families. If you can give me some more information of what you’re trying to do I might be able to help out.

Pat

3

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.