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Reported by: Dail
This one is not in NCBI Taxonomy. The original tip label is 'Caecitellus parvulus A0665 AY827848' and the Genbank accession record maps to the taxon Caecitellus parvulus.
The 'descr…
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I am trying to convert a Genbank file to GFF3 following the latest version of the official [specification](http://www.sequenceontology.org/gff3.shtml). Here is an example of Genbank file I need to con…
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Would it be possible to add an additional annotation element "GenBankCode" and if possible find a way to automatically discover and code it?
![image](https://user-images.githubusercontent.com/46099…
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Hello
I have a problem with download and summarize NCBI Dump files as below:
> (base) amugae1210@pc101:~/tools/PhyloPlus$ ./phyloplus.sh -m download
cd /home1/amugae1210/tools/PhyloPlus
mkdir …
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This happens:
```R
> name2taxid("s2")
"164330"
> name2taxid("s2") %>% taxid2name
"Thauera aminoaromatica"
```
S2 is a strain name for this bacteria. See [here](https://www.ncbi.nlm.nih.gov…
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All iNat Observation fields are listed in the initial comment.
But some should (also) be mapped to MO fields
###Tasks
- [x] Review iNat obss in [2023 NEMF List](https://docs.google.com/spreadsheets/d…
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The NCBI is phasing out GI numbers per this [announcement](https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/). The code works for now but [`vdb.parse`](https://github.com/blab/next…
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The current implementation of the SBOL/Genbank converter in sbol3_genbank_conversion.py uses a custom class `Location_GenBank_Extension` to represent GenBank's fuzzy location field.
Unfortunately, …
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Hi,
is it possible to use `phylotaR` also for retrieving orthologous protein sequences (using all-vs.-all blastp searches) from Genbank/NCBI?
Many thanks in advance for your help!
Jan
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https://www.ncbi.nlm.nih.gov/genome/plasmids/154?
awk -F"\t" '{print $7}' genomes_plasmids.txt -- for genbank $7, for refseq $6
esearch -db nucleotide -query CP007178 | efetch -format fasta > te…