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Protocols

SPARCLE specifications

Information


Unique identifier OMICS_14228
Name SPARCLE
Alternative name Subfamily Protein Architecture Labeling Engine
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Aron Marchler-Bauer

Publication for Subfamily Protein Architecture Labeling Engine

SPARCLE citations

 (4)
library_books

Phyletic Distribution and Lineage Specific Domain Architectures of Archaeal Two Component Signal Transduction Systems

2018
J Bacteriol
PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] The domain architectures of the archaeal RRs were manually checked against the CDD/SPARCLE and InterPro databases (, ). The RRs that contained, in addition to the REC domain, unassigned regions of ≥70 amino acid residues were marked as containing putative novel output domains (Table […]

call_split

Interdependence of Primary Metabolism and Xenobiotic Mitigation Characterizes the Proteome of Bjerkandera adusta during Wood Decomposition

2018
Appl Environ Microbiol
PMCID: 5752865
PMID: 29101201
DOI: 10.1128/AEM.01401-17
call_split See protocol

[…] NCBI BLASTP (using a BLOSUM62 matrix), using only fungal sequences from the nonredundant protein database, with an E value cutoff of <1e−5. To characterize the proteins with unknown function, the CDD/SPARCLE domain analysis function () on NCBI was used to generate a map of any domains. Domain identifications on CDD had an E value cutoff of <1e−03, but each domain was also manually curated for accu […]

library_books

Cloning and Molecular Characterization of an Alpha Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi

2017
Life
PMCID: 5745559
PMID: 29160840
DOI: 10.3390/life7040046

[…] The predicted amino acid sequence of the putative glycosyl hydrolase from Hqrw_2071 was screened for the presence of functional domains using the NCBI’s CDD/SPARCLE Tools []. In order to detect functional features with respect to protein structure, the COBALT program [] was used to generate an anchored multiple sequence alignment (MSA) based on functional […]

library_books

What is the difference between the breakpoint graph and the de Bruijn graph?

2014
BMC Genomics
PMCID: 4240671
PMID: 25572416
DOI: 10.1186/1471-2164-15-S6-S6

[…] alternating between 3 colors, where the third color corresponds to repeated elements (see Figure ). Nurk and Pevzner [] recently used this framework to develop a new comparative genome analysis tool SPArcle and applied it to analyzing multiple bacterial strains resulting from the "controlled evolution" experiments []. SPArcle is based on SPAdes assembler and, in difference from Cortex, it uses id […]

Citations

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SPARCLE institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
SPARCLE funding source(s)
This work was supported by the Intramural Research Program of the National Library of Medicine at National Institutes of Health/DHHS.

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