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Bioinformatics

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Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

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biopython / biopython

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PDBParser and MMCIFParser assign HETATM ids differently

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JoaoRodrigues
JoaoRodrigues commented Sep 11, 2020

This issue comes from the benchmark in #3230.

The first item in the residue id of HETATMs is "H_" + res.resname. Because the PDB format is a column-delimited format, we don't strip the empty spaces around residue names with less than 3 characters (e.g. MG) and end up with something like H_ MG in the id. The MMCIFParser, on the other hand, does strip this whitespace so we end up with H_MG

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seandavi / awesome-single-cell

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Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

python bioinformatics analysis clustering gene-expression data-visualization dimensionality-reduction awesome-list data-integration atac-seq single-cell rna-seq-data scrna-seq-data cell-cycle cell-differentiation gene-expression-profiles analysis-pipeline cell-populations rna-seq-experiments cell-clusters
  • Updated Sep 8, 2020
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