PIRSF statistics

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Associated diseases

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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 in pipelines

 (2)
2017
PMCID: 5514137
PMID: 28717205
DOI: 10.1038/s41598-017-05085-7

[…] 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, […]

2016
PMCID: 5381511
PMID: 28172869
DOI: 10.1093/gbe/evw273

[…] l. clavipes genome in the following databases: tigrfam 13.0 (), prodom 2006.1 (), smart 6.2 (), hamap 201311.27 (), prositepatterns 20.97 (), superfamily 1.75 (), panther 9.0 (), gene3d 3.5.0 (), pirsf 284 (), pfam-a 27.0 (), prositeprofiles 20.97 (), and coils 2.2 (). for proteins with matches, we extracted the gene ontology (go) terms. we used orthomcl-db () to assess orthology of gene […]


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PIRSF in publications

 (74)
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, […]

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

[…] 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 […]

PMCID: 5517455
PMID: 28775722
DOI: 10.3389/fmicb.2017.01380

[…] 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 […]

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

[…] 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, […]

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

[…] 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 […]


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

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