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- [ ] Database integration
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Hi,
Is there a way to request NCBI or Uniprot accessions and/or the functions of the target proteins using foldseek api ?
with the python command : result = get('https://search.foldseek.com/api…
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I'm encountering an issue where certain identified regions from the Phaster analysis of my sequence (available at https://phaster.ca/submissions/NC_019418) are not appearing in the output, despite bei…
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Hi,
First of all thank you for this R package, it's a really useful tool.
Nevertheless I have an issue when I use the following script to find my sequences in Genbank:
**install.packages("Ann…
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checkV paper: https://www.nature.com/articles/s41587-020-00774-7
The checkV database is a superset of GenBank viral. This may improve taxonomic identification for viruses.
Potential problems -- …
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Hello!
Thanks a lot for making this tool available. I ran the demo and analyzed the sample dataset with no issues but when testing charcoal on my own dataset I am running into errors which seem to…
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https://wiki.flybase.org/wiki/FlyBase:Links_to_and_from_FlyBase#Links_from_FlyBase
Links from FlyBase
FlyBase supports linkouts from any FlyBase object that has a stable FlyBase ID (e.g. FBxx[0-…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…
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First I want to thank you for this great tool!
I wanted to ask if there was an option to get the metadata file for a list of accessions without downloading the genomes. I would like to refine the n…
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As part of #2046 we are moving from ``Seq`` objects having an alphabet object from ``Bio.Alphabets``, to recording the molecule type in the ``SeqRecord`` annotations instead. Currently this recycles t…