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Homology search started at 2024-08-21 08:40:06.163220.
Settings:
Search method: diamond.
Self-alignment method: native.
Remote fetch enabled: no.
Reading input proteins...
Sulfurospirill…
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Hello every one,
I'm, trying to run the tool. However, after creating the DB via the mmseqs2 by my download NR.fasta that I had before, I run the homology search and I failed, and the feedback like …
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Hi there,
Should I specify an evalue for the hmmscan for Including homology searches as ORF retention criteria? In the tutorial, you didn't specify a evalue: `hmmsearch --cpu 8 --domtblout pfam.dom…
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Dear author, I have a question about how to succeed my analysis. I make a directory named "deduce" and download three genomes from NCBI. Then, I entered the following command, but it did not work cor…
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Hello,
Thank you for providing this software! However, I encountered the following error when using phase_contacts_with_monte_carlo:
[0h 0m 0s] Loading GFA...
No index found, generating .gfai f…
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Idea: find a few examples of homology RRIs in human and mouse training data. Homologe x of the mouse can be then tested if it will be correctly predicted by the 'human model' and vice versa.
TODO…
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Hi, nice work! We encountered a problem using your project.
1. I'm having a lot of conflicts using `conda env create -f environment.yaml`.
2. Do I have to download uniref100 to run tests on my ow…
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- [x] curate depolymerase protein database (remove redundancies, construct tree,...)
- [ ] extend and curate depolymerase database by homology searches in IMG VR 3
- [ ] identify (blast) depolymeras…
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Hello. great tool!
I´m actually using Acrfinder, but I would like to know if the homology search considers all described, verified Acr proteins.
Thank you in advance.
Best regards.
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Dear Brian,
I am annotating a lizard genome by combining GeMoMa (Homology-based), AUGUSTUS (ab initio prediction), and StringTie (transcription-based). Since the transcription was from only uterus …