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Hi Jon,
I am running funannotate in a conda env created recently, But when I executed the test commands "funannotate test -t all --cpus 5", It reported an error, What should I do to make funannotate …
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Several mongo queries are really slow which occasionally can cause timeout issues for users.
The general issue are that many queries uses $and/$or statements which require mongo to evaluate all cas…
mhkc updated
11 months ago
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Hello.
I want to use EquiPNAS to check my TF bing sites (picked up from RNA seq experiment).
After creating the environment with conda, I downloaded the published models and tested the operation.…
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https://doi.org/10.1109/BIBM.2016.7822515 (https://arxiv.org/abs/1611.05777)
> Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promot…
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https://doi.org/10.1101/103994
> As high-throughput biological sequencing becomes faster and cheaper, the need to extract useful information from sequencing becomes ever more paramount, often limit…
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Can this model be used to generate features for a large number (more than 10,000) of protein sequences, and is there an improvement after trying the low efficiency of the model prediction?
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…
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**Are you using the latest release?**
`funannotate v1.8.11`.
**Describe the bug**
funannotate test is failing at the predict step with error "Not enough gene models 175 to train Augustus (200 re…
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After migrating from [bio_embeddings](https://github.com/sacdallago/bio_embeddings) to calculate embeddings directly in biotrainer for the provided sequences, it is now theoretically possible to allow…
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Dear Suoqin，
I would like to ask you a question：Why haven't we utilized single-cell proteomics for cell communication recognition and prediction? Isn't protein a more direct reflection of the final p…