GraphML files for sequence networks of PETases and PURases

Version 1.0
Buchholz, Patrick C. F., 2021, "GraphML files for sequence networks of PETases and PURases", https://doi.org/10.18419/darus-2054, DaRUS, V1
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Description
The GraphML files contain the sequence networks and annotated metadata for protein sequences.
Subject Medicine, Health and Life Sciences
Keyword Alignment, Network, Amino Acid Sequence, Graph, Protein Sequence, Sequence Clustering
Notes The GraphML attributes for the edges comprise the edge weights (pairwise sequence identity, "weight"). The GraphML attributes for the nodes comprise the identifiers from the ExED ("sequence_id", "protein_id", "hfam_id", and "sfam_id" for sequence, protein, homologous family and superfamily identifiers, respectively), the NCBI taxonomy ID ("tax_id"), the annotated (organism) source name ("tax_name"), the taxonomic lineage of the source organism ("lineage", with taxa separated by "<--"), and the length of the amino acid sequence ("sequence_length"). In addition, suggested color names are given for both fill color and border color of each node ("color" and "color_border").
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CC BY 4.0

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PET_local_08_55sim.graphml
GraphML Network Data - 5.8 MB
Published Dec 1, 2021
29 Downloads
MD5: abddf6c05feb40d68c3c5cbed3f21d2b
Protein sequence network for PETase homologues. Edges were selected at a threshold of 55% pairwise sequence identity.
Sfam11_09_60sim.graphml
GraphML Network Data - 557.2 KB
Published Dec 1, 2021
23 Downloads
MD5: 7cd626f025e5d7a0a253281649894b7f
Protein sequence network for PURase homologues from LED superfamily 11. Edges were selected at a threshold of 60% pairwise sequence identity.
Sfam13_09_60sim.graphml
GraphML Network Data - 16.2 KB
Published Dec 1, 2021
20 Downloads
MD5: e93342540254b2c25b2826343947b22b
Protein sequence network for PURase homologues from LED superfamily 13. Edges were selected at a threshold of 60% pairwise sequence identity.
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