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sequence-analysis

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biotite

biotite-dev / biotite

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Wrong bonds in structures with residues sharing the same residue ID

padix-key
padix-key commented Jun 3, 2021

Both mmtf.get_structure() and connect_via_residue_names() assign too many bonds, if two adjacent residues share the same residue ID. An example is LEU/ILE 25 in 1JXT. In this case all terminal hydrogen atoms are connected to the respective carbon atom of both LEU and ILE. The reason is that both function iterate residue-wise over the structure and consider both residues as the same res

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good first issue

CSBiology / BioFSharp

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Add pretty printers for common biological file formats

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kMutagene
kMutagene commented Dec 1, 2018

As analyzing biological data with BioFSharp involves a lot of scripting, optional pretty printers help a lot when looking at results directly in the fsi window. This should be especially easy to add for parsing libraries that can already write the correct file format. A basic pretty printer for biocollections is already impelemented.
Here are some formats from the top of my head, feel free to add

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good first issue project-all up-for-grabs

vitaliy-ostapchuk93 / disease-pattern-miner

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Disease Pattern Miner is a free, open-source mining framework for interactively discovering sequential disease patterns in medical health record datasets.
data-science machine-learning data-mining research big-data data-visualization datascience webapp data-analysis research-tool pattern-recognition datamining healthcare-application icd-9 medical-informatics sequence-analysis icd sequence-mining disease-prediction
  • Updated Mar 21, 2019
  • Java

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