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While the `/filtering_terms` endpoint provides a standard way to inform about terms being used/queryable for a beacon there is currently no information about supported genomic variation query paramete…
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Hi,
I am attempting to annotate a customized VCF file using NCBI's GFF and (fna) FASTA files for the Newcastle disease virus (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_004786615.1/). However, …
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Hi
Several BiGG models are invalid in SBML format:
- "listOfFluxObjectives cannot be empty"
e.g. iMM1415, iSynCJ816, iAT_PLT_636, iRC1080
Some models have no objective functions (see #333), but …
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#### Background:
Encountered multiple `unexpected EOF` errors while attempting to download the RefSeq genomes of Actinopterygii (taxon id: 7898) using `datasets` version 15.30.0.
#### Steps to …
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## Expected Behavior
Searching proteins against a database with similar and exact proteins (from bacterial refseq proteome) should return hits with similar and exact matches.
## Current Behavior
Ru…
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Any fix that could be recommended? It runs fine with 800 files
COMMAND:
`python corecruncher_master.py -in SA_proteins -out SA_proteins_out_80_100u -ref GCF_900475245.1_43024_E01_protein.faa -freq 8…
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Dear Developers,
We recently used sistr to serotype some salmonella samples. We realized that the Sistr serovar overall prediction is different from the RefSeq match. In such instances, which serov…
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I am annotating the fungal genome. Can the RNA fasta files from the same family in NCBI's Refseq be combined (redundant data) and then provided to the "funannotate predict --transcript_evidence" param…
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I installed via:
```
conda install -c bioconda refseq_masher
```
But I can't seem to get `contains` to work:
```
-> % time refseq_masher contains --top-n-results 50 -p 12 gut_bridge_sequen…
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Hi
When i supply a gff and fna file the web FACoP.v2 dose not seem to recover the locus_tags from the gff file (in the attributes column). it is assigning its own locus_tags called prodigal_1_xx
…