Aligned fasta file for fungal ITS sequences

Kaur, Jaspreet

unread,

Sep 10, 2015, 2:34:48 PM9/10/15

to Qiime Forum

Hi,

Does anyone have an aligned fasta file of fungal ITS sequences ? that can be used as template to align the sequences.

I would appreciate if you can share it or send me a link if its available online.

Jass

Colin Brislawn

unread,

Sep 10, 2015, 4:48:34 PM9/10/15

to Qiime Forum, jaspre...@ttu.edu

Hello Jass,

UNITE is the go-to database for fungal ITS reads: https://unite.ut.ee/repository.php

I'm not sure if UNITE includes a NAST alignment like greengenes includes. My memory is that the ITS region does not align nearly as well as the 16S regions do, so this may be a problem.

You could also try a reference independent alignment, like those created by MUSCLE. You can do that through qiime using align_seqs.py -m muscle.

Colin

Kaur, Jaspreet

unread,

Sep 10, 2015, 4:56:33 PM9/10/15

to Qiime Forum

Thanks Colin for writing. Unfortunately UNITE doesn't have aligned fasta files. I am trying MUSCLE, but its taking forever.

Regards,

Jass

From: qiime...@googlegroups.com <qiime...@googlegroups.com> on behalf of Colin Brislawn <cbr...@gmail.com>
Sent: Thursday, September 10, 2015 2:48 PM
To: Qiime Forum
Cc: Kaur, Jaspreet
Subject: [qiime-forum 1.9.0] Re: Aligned fasta file for fungal ITS sequences

--

---
You received this message because you are subscribed to the Google Groups "Qiime Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qiime-forum...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Reply all

Reply to author

Forward