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python is a programming language, widely used in bioinformatics

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I am very new to the BioInformatics as my past experience is related to Software Eng. I am working on a protein-RNA binding prediction model and need to filter my Test Set against my Training Set to ...
Ayush Chhangani's user avatar
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I'm working with the PANTHER DB API to analyze gene functions and want to categorize specific molecular functions into broader PANTHER pie chart categories for visualization. What I've done: Used ...
Ahmed Alagha's user avatar
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I am trying to make a python script that allows me to get an already generated alignment from clustal W online, introducing the sequences of a set of primers and getting an HTML with all the sequences ...
eduardobabiano's user avatar
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I need a dataset of Non-Ribosomal Peptide Synthetases (NRPSs) for my research. I think it should be there on antiSMASH but unfortunately after trying many types of queries (here) I was not able to get ...
Ilia Kipshidze's user avatar
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I have been generating Snakemake sample tables from a GEO identifier (GSExxxxxx) directly by making requests to the NCBI and ENA APIs. It works, but with some caveats (explained in this open question: ...
Freek's user avatar
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I have made a Python function that can turn an NCBI GEO identifier (GSExxxxxx) into an ENA bioproject accession using the NCBI API. I need this to get sample tables which I then feed into Snakemake. ...
Freek's user avatar
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I am new to Bioinformatics and want to know if this is possible. I have a .txt file with a series of 50 gene sequences and I want to know if I can find the identity of them iteratively through a ...
Kalyan Ghadiyaram's user avatar
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According to HBPLUS, 5i55.pdb has 44 hydrogen bonds. ...
user366312's user avatar
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I have mitochondrial heteroplasmy data obtained from ddPCR that I am trying to group into age bins. One bin edge has to be 0. I would like to dynamically choose all the other bin edges. Each bin ...
Matt Aruta's user avatar
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I am trying to install DCA but it fails due to dependency issues. The package is no longer being maintained. Following are the commands I need to run: ...
user2998764's user avatar
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I am modifying bpps.py in the Arnie Python package to integrate LinearFold for RNA secondary structure predictions. However, I keep encountering "KeyError: '...
Hugh Redford's user avatar
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1 vote
1 answer
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I am trying to configure Arnie to work with LinearFold, LinearPartition, and ensure that bpps.py integrates properly. However, I’ve encountered multiple issues regarding ViennaRNA path detection, ...
Hugh Redford's user avatar
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I am an undergraduate student trying to understand the working of Apta-MCTS (https://pmc.ncbi.nlm.nih.gov/articles/PMC8232527/). I believe that initially, I have to run the preprocess.py file first ...
Corporeal Patronus's user avatar
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We ran into an issue with pycoQC this week that we spent a stupid amount of time resolving. Someone reported a related issue on the ...
Mark Ebbert's user avatar
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I am running vSNP step 2 and it is saying that the process completed and that it saved the VCF files in default files but I can't find any output. I'm not getting any errors either. Here is my script: ...
Lucy Kelly's user avatar
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