Analisis of FUNGI with UNITE database in Mothur

Hi all,
I’m a PhD student, just at the begin with mothur analysis… I got a problem when I have to align sequences usign “align.seqs” comand.

I downloaded the database of fungi from UNITE website, but I didn’t find the “aligned file”.

I tried to process align.seqs comand with all file found in the UNITE directory dowloaded, as:
UNITEv6_sh_97.fasta
UNITEv6_sh_99.fasta
UNITEv6_sh_dynamic.fasta

But none is working…please can you help me?
Any help will be very apreciate

best regards to all

Sara

Assuming you have 18S rRNA gene sequence data, you would probably want the eukaryotic silva database that we have posted

https://www.mothur.org/wiki/Silva_reference_files

Pat

Hi Pat, thank for replying.

I obtained sequences from 18S-ITS1-5.8S regions of fungi, and now I’m trying to process data with Mothur!

I thought that in UNITE folder there was the align.file and when I didnt find it I was in doubt!

Regards

ITS can’t be aligned across all fungi because there’s too much evolution. Here is my batch for processing ITS2 seqs with mothur.

I’ve never worked with ITS1 data so don’t know how well UNITE covers that region, you may be better off with Silva

Hi Path,

Really thank for your recommendation!! We have also primers to amplify the ITS2 region, but as we are at the begin of fungi analysis, I’m trying to test different software package in order to understand if I will be able to work with fungi :slight_smile:

Thank again!

sara

Hi Patrick,

Really thank for your recommendation!! We have also primers to amplify the ITS2 region, but as we are at the begin of fungi analysis, I’m trying to test different software package in order to understand if I will be able to work with fungi :slight_smile:

Thank again!

sara

1 Like

Hi Patrick,

Really thank for your recommendation!! We have also primers to amplify the ITS2 region, but as we are at the begin of fungi analysis, I’m trying to test different software package in order to understand if I will be able to work with fungi :slight_smile:

Thank again!

sara

Dear Patrick,

When I run a command I get a Logfile; but every time I run the same command again, the previous logfile is deleted…

Is it normal?

are you renaming the logfiles? they should be named with a time stamp which makes each filename unique

I’m not renaming the logfiles actually. I will do it from now!

Thanks!!

It works! Now I have more than one logfile!
just last question… I’m trying to analyse 16S using this procedure but mothur stop all time at the command classify.seqs

#unique.seqs(fasta=current)

#count.seqs(name=current.names)

#align.seqs(candidate=current.fasta, template=\SILVA_128_mothur\silva.seed_v128.align)

#filter.seqs(fasta=current)

#unique.seqs(fasta=current.unique.filter.fasta, name=current.names)

#pre.cluster(fasta=current.unique.filter.unique.fasta, name=current.names)

#Chimera.vsearch procedure:
vsearch --derep_fulllength
vsearch --cluster_fast
vsearch --sortbysize
vsearch --uchime_denovo
*Using fasta.file, obtained by vsearch --uchime_denovo, I try to run the classify.seqs command.

#classify.seqs(fasta=current, reference=\SILVA_128_mothur\silva.seed_v128.align, taxonomy=SILVA_128_mothur\SEED\silva.seed_v128.tax, output=simple)
*The command is not working, because mothur stop and close the run.

In the logfile there is no explanation about why mothur is closing, and I don’t understand why…

Can you help me?

Really thank for your help…

Best regards

do you get any errors? you’re telling it to look in 2 different locations for your reference and taxonomy, are they really in different folders?