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I was super curious to try this out on my favorite discrete data: protein sequences! I created a simple dataset class following the existing code:
https://github.com/dacarlin/protein-sedd/blob/mai…
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Hi,
Hope that seqkit can extract transrcipt/cdna/gene/protein sequences from references fasta and gff/gtf file. gffread can do this but it can not handle large chromosomes correctly.
Best,
Kun
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Hi developer,
thank you for this nice tool! I wonder does it limit the size of faa file for input?
when I enter a long sequence, it turned out error like:OSError: [Errno 36] File name too long:
How…
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* **InterPro ID / label**
GO:0006397 | mRNA processing | IEA with IPR030843
* **Example sequences with problematic annotation (ID + gene/protein name):**
* **Description of issue**
this …
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Hi Zhaohan,
FusionDTI is a fantastic work. I am currently attempting to test it for drug-protein interaction prediction, but I am uncertain how to obtain the Uniprot IDs for all the protein sequen…
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I love Orthofinder, it has been so helpful in our research in so many ways.
I am having one particular issue where I am getting non-informative sequence IDs in all the fastas in the Single_Copy_Ort…
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First, thank you for your excellent research.
Based on your research, I attempted to predict protein-ligand structures (a kind of binding mode analysis) using single protein:single ligand combination…
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* **PTHR ID & PTN node:**
mad2
GO:0005654 | nucleoplasm | IBA with Q5BAB9 , PTN000217420 , FBgn0035640 , Q13257 , WBGene00003161
* **Sequences with problematic annotation (ID + gene/protein…
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Hi, I have a corpus of about 500,000 protein sequences and would like to apply them to existing models like ESM2 or this one for predicting the fitness effect of changing an amino-acid for another.
H…
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* **PTHR ID & PTN node:**
ALANYL-TRNA SYNTHETASE (PTHR11777)
PTN000206953
* **Sequences with problematic annotation (ID + gene/protein name):**
FBgn0027094 AlaRS
* **Type of Issue: Erroneous sou…