ATP-cone sequence clusters
type: Dataset
description: The NCBI RefSeq database (2019-03-19; Haft et al. 2018 https://doi.org/10.1093/nar/gkx1068) was searched with Pfam's ATP-cone profile (accno: PF03477; Finn et al. 2010 https://doi.org/10.1093/nar/gkp985) returning 44367 NCBI accessions. Ribonucleotide reductase proteins were identified using HMMER (Eddy 2011 https://doi.org/10.1371/journal.pcbi.1002195) profiles from the RNRdb database (http://rnrdb.pfitmap.org). Subsequently, sequences were clustered with UCLUST (Edgar 2010 https://doi.org/10.1093/bioinformatics/btq461) at identity to remove sequence duplicates (24477 sequences remaning). All sequences were pairwise aligned to each other using LAST (Kiełbasa et al. 2011 https://doi.org/10.1101/gr.113985.110) and a bitscore matrix was constructed. The bitscore matrix was clustered with MCL (Enright, Dongen & Ouzounis 2002 https://doi.org/10.1093/nar/30.7.1575) using the Cluster Maker 2 (Morris et al. 2011 https://doi.org/10.1186/1471-2105-12-436) Cytoscape (Shannon et al. 2003 https://doi.org/10.1101/gr.1239303) app. Bitscores < 200 were not included in the initial network and an inflation parameter of 2.5 was used. The file "atp-cone_mcl_clustering.tsv" contains all information necessary to recreate the clustering as well as the assigned cluster numbers to each sequence. Column names: SUID: Cytoscape's id, accno: NCBI's accession number, mcl2.0ewc200-mcl3.0: cluster assignments with inflation parameters and bitscore cutoff (ewc; when used), name: sequence identifier composed of accno plus cone number, outer_inner: "inner", "middle" or "outer" when more than one cone present in full sequence, pclass and psubclass: RNR class and subclass, ptype: protein type, taxon, tdomain: taxonomic domain, title: NCBI's description of the sequence. The "precluster_assignments.tsv" file contains the results of the preclustering with USEARCH, i.e. which usearch cluster (first column) each accession number (second column) belong to.
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Daniel Lundin
date modified: 2019-04-05
date published: 2019-03-25
keywords: Biochemistry
  type: DefinedTerm
  term code: 10408
license: https://creativecommons.org/licenses/by/4.0/
publisher: Stockholm University
version: 0

PropertyValue
property ID: DOI
value: 10.17045/STHLMUNI.7886641

Daniel Lundin
type: Person

Stockholm University
type: Organization