Question: SEED analyses in MEGAN: How to connect Seed database with blast data
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gravatar for Bumble
3.3 years ago by
Bumble10
Bumble10 wrote:

I would like to use SEED to identify functions in a metegenomic dataset. I have downloaded the latest SEED mapping file here, translated sequence data to proteins, performed a blastp against RefSeq protein files downloaded from NCBI and imported the data into MEGAN. Taxonomy assignment works, but SEED does not show any hits. I assume that my sequences cannot be connected to the Seed database.

The blast command I use is

blastp -db Prot_DB.faa -query SampleProt.fasta -evalue 1e-5 -max_target_seqs 1 -outfmt 5 -out ProtBlastResults.txt -num_threads 12

What am I doing wrong? And is there a detailed tutorial on how to prepare data for SEED analyses in MEGAN? Any help would be greatly appreciated!

seed blast metagenome megan • 1.4k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 3.3 years ago by Bumble10

Hi, did you ever figure this issue out?

ADD REPLYlink written 16 months ago by gangiaht0
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