Extract sequences of OTUs

Commands in mothur
1

Dear all,
I have analyzed my data following the “Costello stool analysis” almost to the letter, so now I have a large table with samples in the rows and OTUs in the columns, and inside the table itself are the numbers (abundance) of sequences from each OTU at each sample. That is great, but now I want to get the actual FASTA sequences, something like:

Sample FOREST:
OTU13
Seq #1: aagtgctacct… etc.
Seq #2: ggtgacccatc… etc.
OTU8
Seq #1: aagcccaacct… etc.
Sample DESERT:
OTU10
etc…

Any help would be much appreciated!
P.

2

You may want to check out the bin.seqs command. You would run bin.seqs(list=yourListFile, fasta=yourFastaFile, group=yourGroupFile). The output would look like: sequenceName group otu#.

AY457723 C 1
ACGCTAGCGACAGGCTANACACATGCAAGTCGAGGGGCAGCACAGGTAGCAATA…
AY457687 C 1
TGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAGGGGG…
…