Help with ARB database and make a ecoli_v3.fasta file

1

Hi all, I’m very new to bioinformatics and I need some help :frowning:
I’m trying to access the ARB website following the tutorial but it gives me error:

Error: Can’t open display: :0
ARB: Loading ‘ntree.arb’
ARB: Loading ‘/home/maxine/miniconda3/lib/arb/lib/arb_default/ntree.arb’ done
Using properties from ‘/home/maxine/miniconda3/lib/arb/lib/arb_default/status.arb’
[arb_launcher[0]: ‘arb_ntree SSURef_NR99_123_SILVA_12_07_15_opt.arb’ has terminated with error 1]
No protocol specified
Error: Can’t open display: :0
[arb_launcher[0]: Still have 1 arb processes…]
[arb_launcher[0]: All launched processes terminated]

Also, how do I save the v3 sequence of E.coli on a file to then align? (Unfortunately I’ve sequenced v3-v4 region)

2

Hi Maxine -

You shouldn’t need to use ARB to make a v3 sequence from E. coli. If you go to this tutorial, you’ll find the E. coli sequence is provided. You can use that.

In fact, the example I use is to generate the V3 region of the sequence.

Pat

3

Hi Pat!
Thanks so much for your quick reply, I did use e.coli sequence at the end and it worked. Thanks!