Representative sequence

Commands in mothur
1

Hi,

Using bin.seqs command, i obtained different files containing fasta sequences of each reads with the corresponding OTU (unique, 0.01, 0.02 etc. see example below)
Now i want cluster each read sequence of this file in order to get a representative sequence wthout using get.oturep or make.database commands.
Did you know how make this ?

Thanks in advance

Alex


[u]example:[/u] _>M00611_3_000000000-A6TJ7_1_1102_22861_6373 Otu00001 CCT--AC-G-G-G-G-G-GC-A-GCAGT-G-A-GG-A-A-TA-TTGG-T-C--AA-T-G-G--TC-GG-G--A-G-A-C-TG-A-A-C-C-A--GC-C-A-A-GCC-G-C-G-T------G-A-G--G--GA----A-G--A--A--G-G-TA-----C----AG-CG-----T-A-T-------C-G-T--A---AA-C-C-TC---------------------TT-TT-G-C--C-GGG----G--A-A--C---AA-GAGC-T---T-C-C--A--------------------C--------------------------GA--------------------------G-----------------------------T-GGG-A-GT-G-T-G-A-G-C-----G-T---A-C-CC--------G-G-A-G---------A-A-----------A--AA---------GC- >M00611_3_000000000-A6TJ7_1_1115_7616_15647 Otu00001 CCT--AC-G-G-G-A-G-GC-T-GCAGT-G-A-GG-A-A-TA-TTGG-T-C--AA-T-G-G--TC-GG-G--A-G-A-C-TG-A-A-C-C-A--GC-C-A-A-GCC-G-C-G-T------G-A-G--G--GA----A-G--A--A--G-G-TA-----C----AG-CG-----T-A-T-------C-G-T--A---AA-C-C-TC---------------------TT-TT-G-C--C-GGG----G--A-A--C---AA-GAGC-T---T-C-C--A--------------------C--------------------------GA--------------------------G-----------------------------T-GGG-A-GT-G-T-G-A-G-C-----G-T---A-C-CC--------G-G-A-G---------A-A-----------A--AA---------GC-A--TC-G---G-C-TAA-C-T-C-C--G-T--G-C-CA-G-C-A-G-C--CG-C---GG--TA-AT--AC---GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT---TT-A--AA-GG-GT-GC--G-TA-G-G-C-G---G-C-GA-G-T-T-AA-G-T-C-A--G-C-G-G--TA-A-AA-GC-C-C-GG-G-G-------CT-C-AA-C-C-C-C-G-G-C---C-C-G--C-C-G-T--T--_
2

You don’t need the results of the bin.seqs command to use the get.oturep command, Redirecting…. You want to run something like this:

mothur > get.oturep(column=yourDistanceFile, count=yourCountFile, fasta=yourFastaFile, list=yourListFile, label=yourLabel)

The resulting *.rep.fasta file will look like: RepSequnceName OtuName|OtuAbundance|GroupsPresentInOTU

GQY1XT001CYVBA Otu0001|6129|F003D000-F003D002-F003D004-F003D006-F003D008-F003D142-F003D144-F003D146-F003D148-F003D150
C-G–T-T–GA-A-A-C-T-G-G–TT-T-T-C–T-T-G-A-G-T-G-A-GC-GA-G-A-A-G-T-A–TG-C-GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA–TG-C-AT-AG–AT-…
GQY1XT001C44N8 Otu0002|4936|F003D000-F003D002-F003D004-F003D006-F003D008-F003D142-F003D144-F003D146-F003D148-F003D150
C-G–T-T–GA-A-A-C-T-G-G–CG-T-T-C–T-T-G-A-G-T-G-G-GC-GA-G-A-A-G-T-A–TG-C-GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA–TG-C-AT-AG–AT-A-…
GQY1XT001A2EZX Otu0003|4871|F003D000-F003D002-F003D004-F003D006-F003D008-F003D142-F003D144-F003D146-F003D148-F003D150
C-G–T-T–GA-A-A-C-T-G-G–GA-G-C-C–T-T-G-A-G-T-G-C-GC-GA-G-A-A-G-T-A–GG-C-GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA–T…

Mothur will also generate a *.rep.count_table.

3

Thanks westcott for your answer.

The issue is that i don’t want use get.oturep command because it tooks too many time to get the .dist file. i tried with method=abundance but the software run… run… run… and nothing happened.

Alex