nr database fungi

[Pol2021]

Dear All,

how can I filter out only fungi hits from the nr protein database?
Thanks a lot

[BasesBreaker]

Pol2021 I used to do some mycology work so I'll try to help. Filtering out only fungal hits from the NCBI's non-redundant (nr) protein database should be relatively easy.

If you're using NCBI's BLAST or similar tools, you can restrict your search to fungi by including a taxonomic identifier in your query. For fungi, the taxonomic ID is `4751`. Your query might include something like `txid4751[Organism:exp]` to restrict to fungal organisms.

If you have downloaded the nr database locally and are using tools like BLAST+ or other sequence analysis software, you can create a custom database that includes only fungal sequences.

- Download the taxonomic information from NCBI.
- Extract the identifiers for fungal sequences (you'll again use the taxonomic ID `4751`).
- Create a custom database using only those identifiers.

Another way would be to run your analysis against the full nr database and then filter the results using the taxonomic information.
- BLAST results, for example, can include taxonomic information if you format the database with the appropriate taxonomy files.
- You would then post-process the results to include only hits that are classified under the taxonomic ID for fungi.

Let me know if this helps.

[Pol2021]

Dear BasesBreaker,

thanks a lot for the feedback. Yes, I use NCBI BLAST, and I also have the nr database already locally. Indeed the ID is the way, but can you give the command line to do that? The above options 1 or 2 are fine, but I cant define a command line that does that, Thank you.

[friguiAhlem]

dear Pol2021 could you tell me please if you found the command line that permits to
- Download the taxonomic information from NCBI.
- Extract the identifiers for fungal sequences (you'll again use the taxonomic ID `4751`).
- Create a custom database using only those identifiers.