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> Given a list of binomial names, how can I get accession ids and sequences?
```
For each database in ['plant', 'vertebrate', 'invertebrate] do
taxids = restez::list_db_ids() |>
restez::gb…
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I can use the image to create the relative directories and download the example database but I can not download the query db.
$ docker run --rm ncbi/blast efetch -db protein -format fasta \
-id …
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Hi,
I'm currently having problems to store the optimized byte sequence to my postgres database. I keep getting the error `SQLSTATE[22021]: Character not in repertoire: 7 ERROR: invalid byte sequen…
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Hi there
I'm trying to use kraken2 on my samples, after successfully creating a database containing all bacteria, archaea, protozoa and fungi from NCBI.
I created the database in this way and ever…
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On a discussion on different [latex-mathml converters](https://sourceforge.net/p/docutils/patches/197/) I found out about the following test file: https://docutils.sourceforge.io/docs/ref/rst/mathemat…
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Hi,
For some reason the DB is failing to start.. At least 2 weeks before there were no updates or configuration changes. Tried connecting to the DB directly from the DB with the same issue:
```
…
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## Short description of the problem
The `--min-alignment-fraction` parameter of `anvi-dereplicate-genomes` is not working as expected.
## anvi'o version
I'm using the master version as of thi…
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command:
**$ vsearch --db UNITE10.fasta --sintax refs.fasta --tabbedout refs_sintaxonomy.tsv --sintax_cutoff 0.8 --sintax_random**
**vsearch v2.28.1_linux_x86_64, 251.2GB RAM, 96 cores**
produces…
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I'm becoming rather fond of the protein search (#40) and want to combine DNA and protein searches (#48) but keep on running into mental problems about how to deal with taxonomy. This issue is to expla…
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Submitted by: @luronumen
According to the documentation, SEQUENCE is the SQL\-compliant term for what InterBase and Firebird have always called a GENERATOR and SEQUENCE is the recommended syntax fro…