Question: Short read translated alignments using Diamond
0
gravatar for xiaomingjia
2.8 years ago by
xiaomingjia0 wrote:

Greetings!

I'm using Diamond to do translated alignment of a gut microbiome metagenomic sequence dataset agains the human proteome (looking for possible sequence homology and autoantigens).

Question: Diamond seems to only report alignments for sequences of read length more than 51 DNA bps or 17 amino acids. Is there a way to lower this threshold, or is there another method I should try? Ideally I'd like to align sequences of as short as 9 amino acids (approximately the length of peptides presented by MHC).

Best,

Sherman

ADD COMMENTlink written 2.8 years ago by xiaomingjia0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1826 users visited in the last hour