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The locus to gene prediction dataset is loaded to Platform. This dataset is used to populate credible set widget and locus to gene table. This table at this point only contains study locus id, gene id…
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Hi,
First of all, thanks for your benchmark.
I am interested in the raw outputs (predictions) of the methods, especially for the Gene Finding task.
As I prefer to avoid retraining the CNNs, is th…
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Hi, I'm looking to predict genes for my insect genome. For most genes the prediction is working out good, but egapx is missing predictions for some species specific, single exon genes (experiementally…
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The functional impact column should show a gray dot for benign predictions:
See [URL](https://www.cbiopo…
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Should be able to pass in externally derived GFF3 gene model predictions, ie from newer AI/DL/ML methods like helixer and/or Tiberius. But the requirements are too onerous to include as a dependency.…
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I just recently found out about miniprot and have been testing it out as an alternative to MetaEuk in my VEBA metagenomics workflow software suite (https://github.com/jolespin/veba). When I ran minip…
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Regarding the issue of de novo gene structure prediction, it seems that there is no model for watermelon in the Augustus software. Did you build the model yourself? How can one construct a reasonable …
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Hello,
In the supplemental information of the BioRxiv preprint (https://www.biorxiv.org/content/10.1101/2023.02.06.527280v2.supplementary-material) I read that over-prediction in small contigs (small…
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```
phabox2 --task cherry --dbdir '/home/berntm/projects/mb-galaxy-tools/tools/phabox/test-data/phabox_db_v2/' --outpth output/ --contigs '/tmp/tmpj_qx6mfj/files/a/c/9/dataset_ac9084b8-6509-4549-8ba…
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Hello!
I am wondering if the synthetic lethality prediction files are available for the methods that you benchmarked in this work. This would be a very valuable dataset for mining and exploration.…