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Protocols

UniParc specifications

Information


Unique identifier OMICS_03880
Name UniParc
Alternative name UniProt Archive
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline UniProt proteomes Team

Publication for UniProt Archive

library_books

UniProt archive.

2004 Bioinformatics
PMID: 15044231

UniParc citations

 (14)
library_books

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

2018
Microbiome
PMCID: 5863371
PMID: 29562928
DOI: 10.1186/s40168-018-0432-5

[…] NCBI non-redundant protein database, SwissProt and TrEMBL) as well as the S. purpurea 94006 reference genome. During the informed annotation step, Populus trichocarpa reference genome was also added. UniProt Archive (UniParc) database was used to protein blast differentially expressed (DE) contigs that did not have a hit in any of the databases. NCBI nucleotide database was used to nucleotide blas […]

library_books

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

2017
Biotechnol Biofuels
PMCID: 5450047
PMID: 28572841
DOI: 10.1186/s13068-017-0828-7

[…] onsistent, and rich annotation; the section Swiss-Prot contains manually annotated records. The UniRef databases provide NR clustered sets of sequences from the UniProtKB (including isoforms) and the UniProt Archive (UniParc) records (a comprehensive and NR database that contains most of the publicly available protein sequences). Functional domains were identified using the Pfam domain database (P […]

library_books

Minimizing proteome redundancy in the UniProt Knowledgebase

2016
PMCID: 5199198
PMID: 28025334
DOI: 10.1093/database/baw139

[…] or the most representative, we address the challenges that redundancy poses. For those users who want every sequence no matter how redundant, we make all sequences available via the UniProt Archive (UniParc). Our method identifies redundant proteomes by performing sequence comparisons of sets of sequences for pairs of proteomes and subsequently applies graph theory to find dominating sets that pr […]

library_books

Div BLAST: Diversification of Sequence Search Results

2014
PLoS One
PMCID: 4274030
PMID: 25531115
DOI: 10.1371/journal.pone.0115445

[…] eration may be a viable alternative. One can decrease the redundancy of these databases by a preprocessing procedure. Commonly used protein sequence databases such as UniProtKB, UniProtKB/SwissProt , UniParc , and UniRef databases have reduced, non-redundant versions. UniProtKB includes two different databases: UniProt/TrEMBL and UniProt/SwissProt. In UniProt/TrEMBL database, for the fully identi […]

call_split

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

2014
Bioinformatics
PMCID: 4375400
PMID: 25398609
DOI: 10.1093/bioinformatics/btu739
call_split See protocol

[…] f UniProtKB. Production details were previously described (). Briefly, the databases are generated in a hierarchical fashion; UniRef100 clusters are generated first using sequences from UniProtKB and UniParc, UniRef90 clusters are then generated using UniRef100 clusters and UniRef50 clusters are generated using UniRef90 clusters. The clusters are computed using a parallelized version of the CD-HIT […]

library_books

Identification and characterization of three chemosensory receptor families in the cotton bollworm Helicoverpa armigera

2014
BMC Genomics
PMCID: 4112213
PMID: 25027790
DOI: 10.1186/1471-2164-15-597

[…] d using Just_Annotate_My_Proteins (JAMp; http://sourceforge.net/projects/jamps) which is an automated pipelines that 1) used HHblits [] to search against Hidden Markov Models derived from the curated Uniprot archive; 2) assigned controlled vocabulary terms (e.g. GO, KEGG etc.) linked to a Uniprot accession only if an actual experiment provides evidence (i.e. we did not use any ‘inference via elect […]

Citations

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UniParc institution(s)
EMBL Outstation, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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