Using Mothur to analyse amoA gene

Commands in mothur
1

After unique.seqs, I processed dist.seqs and the screen showed:
[ERROR]: your sequences are not the same length, aborting

when I processed summary.seqs:
Start End NBases Ambigs Polymer
Minimum: 1 439 439 0 4
2.5%-tile: 1 480 480 0 4
25%-tile: 1 491 491 0 5
Median: 1 491 491 0 5
75%-tile: 1 491 491 0 5
97.5%-tile: 1 491 491 0 6
Maximum: 1 491 491 0 6

of Seqs: 372

I don’t think it’d be right to simply screen the seqs shorter than 491 bp, whereas I don’t know where to download the suitable aligned template for 491bp-amoA gene to process align.seqs and chimera.slayer

Thank you!

2

You can download representing amoA sequences from NCBI or FunGene web site and align them to create your own database

3

OK, thank you, I’ll have a try.