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Hi,
I've been troubleshooting an issue I've encountered with dnabarcoder's search function when attempting to classify a relatively large number of full ITS sequences (~6000) against the UNITE-INSD …
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The Blast web interface recently switched to a new default database, "core_nt". [info](https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/)
> Effective August 2024,…
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> Maximum number of hits to keep for each query.
>BLAST will choose the first N hits in the reference
database that exceed perc-identity similarity to
query. NOTE: the database is not sorted by
si…
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Hi,
When I run the program providing a reference database it throws an error which I cannot figure out how to solve. Any help is appreciated!
Cheers,
Christoph
/Final processing of outpu…
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## BLAST search
Let's introduce **BLAST** search feature support.
**Displaying BLAST search results for *read*/*feature* sequence**:
- User clicks on *read* (or any other feature) and selects *…
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Hi, thanks for this amazing tool!
I was trying to understand the execution order of database searches. If I got it correctly it is
1. `diamond` on reference proteomes from UniProt, then
2. `blas…
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Dear Mr. Eren,
is it possible to adjust blast in your command line so that uncultured/environmental sample sequences are excluded?
Thanks a lot for oligotyping, great tool!
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Hello,
I have a situation where I am calling `dnabarcoder.py search` multiple times with different query datasets but the reference database stays the same.
Each time I execute the `search` functi…
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OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms
2024-06-02 15:53:19 : Starting OrthoFinder 2.5.5
64 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder a…
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**Background**
For implementation of #381 NGB server shall provide an API to get list of organisms along with `taxids`
**Approach**
NGB server shall provide an API method to search for organisms …