Question: How to identify best-hit taxonomy of many gene sequences efficently
0
gravatar for gwrathe
9 months ago by
gwrathe0
gwrathe0 wrote:

Hello, I have many sequences, each represents a species. I have the aim of identifying these sequences using their best-hit and recording that information to find the relative diversity of my community. I could go on to NCBI refseq and grab the best-hit for each of my sequences and record them but that would be impractical and I know there is a better way! I've heard of people using eFetch or other tools.

Could anyone please help me with recommendations on programs, tools, or instructions on how I can achieve my aim?

Thank you for helping me out! Much appreciated.

ncbi taxonomy sequence gene • 246 views
ADD COMMENTlink written 9 months ago by gwrathe0
4

eutils won't help much unless you search for keywords or accessions. How about sequence searches that give you best hits, with the option to directly give you the taxonomic classification (blastdb5) or LCA (diamond/mmseq2)

blast

diamond

mmseqs2

ADD REPLYlink written 9 months ago by Carambakaracho2.0k
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