PIRSF statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PIRSF
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This map represents all the scientific publications referring to PIRSF per scientific context
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Protocols

PIRSF specifications

Information


Unique identifier OMICS_01697
Name PIRSF
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PIRSF

PIRSF citations

 (104)
library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] each protein sequence. InterProScan v.5.15–55 [] was performed to search protein sequences against a collection of databases including Gene3D v.5.5.0, HAMAP v.201511.02, PANTHER v.10.0, Pfam v.28.0, PIRSF v.3.01, PRINTS v.42.0, ProDom v.2006.1, ProSitePattern v.20.113, ProSiteProfiles v.20.113, SMART v.6.2, SUPERFAMILY v.1.75, TIGRFAM v.15.0 to identify present domains and motifs. Meanwhile, avai […]

library_books

Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β Helical Passenger

2018
Front Microbiol
PMCID: 5767081
PMID: 29375499
DOI: 10.3389/fmicb.2017.02607

[…] ne3D v4.1 (Sillitoe et al., ; Lam et al., ), CDD (Marchler-Bauer et al., ), MobiDB v2.3.2014.07 (Potenza et al., ), HAMAP (Pedruzzi et al., ), PANTHER v11.1 (Mi et al., ), Pfam v30.0 (Finn et al., ), PIRSF (Wu et al., ), PRINTS (Attwood et al., ), ProDom v2012.1 (Servant et al., ), PROSITE v2017.01 (Sigrist et al., ), SFLD (Akiva et al., ), SMART v7.0 (Schultz et al., ), SUPERFAMILY v1.75 (Wilson […]

library_books

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

2017
Sci Rep
PMCID: 5698307
PMID: 29162929
DOI: 10.1038/s41598-017-16186-8

[…] fault parameters, with the exception of sequence E-value (e−10) as well as with InterproScan (ver. 5.18-57.0;) against all the available databases (ProSiteProfiles-20.119), PANTHER-10.0, Coils-2.2.1, PIRSF-3.01, Hamap-201511.02, Pfam-29.0, ProSitePatterns-20.119, SUPERFAMILY-1.75, ProDom-2006.1, SMART-7.1, Gene3D-3.5.0 and TIGRFAM-15.0. Additional information on metabolic pathways was highlighted […]

library_books

Amplicon Sequencing of the slpH Locus Permits Culture Independent Strain Typing of Lactobacillus helveticus in Dairy Products

2017
Front Microbiol
PMCID: 5517455
PMID: 28775722
DOI: 10.3389/fmicb.2017.01380

[…] nalyzed for domains, InterProScan analysis assigned all STs but ST8, ST9, ST10, and ST11, which belong to the slpH2 group, to the Lactobacillus surface layer protein family (InterPro accession number PIRSF037863) using the PIRSF family classification system (not shown). Furthermore, InterProScan identified in all STs the eight motif fingerprints of Lactobacillus surface layer protein family (Inter […]

library_books

Genome reconstruction in Cynara cardunculus taxa gains access to chromosome scale DNA variation

2017
Sci Rep
PMCID: 5514137
PMID: 28717205
DOI: 10.1038/s41598-017-05085-7

[…] ce E value = 1 e−5. Predicted protein sequences were functionally annotated using InterproScan (ver. 5.18–57.0) against all the available databases (ProSiteProfiles-20.119, PANTHER-10.0, Coils-2.2.1, PIRSF-3.01, Hamap-201511.02, Pfam-29.0, ProSitePatterns-20.119, SUPERFAMILY-1.75, ProDom-2006.1, SMART-7.1, Gene3D-3.5.0 and TIGRFAM-15.0). If InterProScan results were available, the domain name, IPR […]

library_books

Time resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection promoting Phytophthora palmivora effectors

2017
BMC Biol
PMCID: 5427549
PMID: 28494759
DOI: 10.1186/s12915-017-0379-1

[…] p search against the GenBank non-redundant (NR) database with e-value ≤10-6; (2) InterProScan (v5.16) search against databases of functional domains (PANTHER, Pfam, Coils, Gene3D, SUPERFAMILY, SMART, PIRSF, PRINTS) with default parameters []; (3) RXLR and EER motif prediction using regular expressions; (4) WY motif prediction based on WY-fold HMM by hmmsearch function from the HMM3 package (http:/ […]


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PIRSF institution(s)
Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, DC, USA

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