oligo issue

Commands in mothur
1

Dear all,

I want to extract only sequences containing specific oligos from a fasta file.

Is this possible in mothur?

2

I think you want the get.groups command, http://www.mothur.org/wiki/Get.groups.

3

Thank you, Westcott, but the get.groups command is not what I want.

I want, for example, to exract sequences containing ATTGCCGTG and TGAAACGTC from a fasta file and make a new fasta file using them.

I somehow managed to do it using ARB sequence editor, but it seems that mothur does not have this function.

4

You may want to take a look at Pat’s SOP, http://www.mothur.org/wiki/Schloss_SOP, which highlights some of the features of mothur. I think what you are looking for is the trim.seqs command, http://www.mothur.org/wiki/Trim.seqs.