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

Information


Unique identifier OMICS_29181
Name PilFind
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages Perl
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mechthild Pohlschroder

Publication for PilFind

PilFind citations

 (16)
library_books

Culture Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

2017
Front Microbiol
PMCID: 5481317
PMID: 28690595
DOI: 10.3389/fmicb.2017.01134

[…] ted to archetypic mono- and diderm cell envelopes, revealed a monoderm cell envelope architecture consistent with other Chloroflexi (Figure ). The genome annotation and specialized searches using the PilFind program () did not reveal any genes associated with flagella, fimbriae or pili, suggesting a non-motile lifestyle. Putative genes associated with spore coat polysaccharide biosynthesis protein […]

library_books

Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome

2017
PMCID: 5397411
PMID: 28473967
DOI: 10.3389/fcimb.2017.00139

[…] of the downstream open reading frames (ORFs) between VPAR_RS05465—5435 have features that are highly reminiscent of type IV prepilins (Figure ). The ORFs in this locus were further analyzed using the PilFind webserver (http://signalfind.org/pilfind.html) (Imam et al., ) and a canonical type IV prepilin leader sequence was detected in VPAR_RS05465. This ORF is also located directly adjacent to the […]

library_books

Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis

2017
PLoS One
PMCID: 5261816
PMID: 28118386
DOI: 10.1371/journal.pone.0170406

[…] ddition, several genes involved in chemotaxis were significantly downregulated in the biofilm cells (Table C in ). Two genes clusters of putative type IV pili biosynthesis genes were identified using PilFind [], including a pil operon (CLJU_c10900 to 10940) and a tad operon (CLJU_c28790 to 28890). These genes were not expressed in the planktonic nor in the biofilm condition (Table D in ), even tho […]

library_books

Comparative Analysis of Type IV Pilin in Desulfuromonadales

2016
Front Microbiol
PMCID: 5174107
PMID: 28066394
DOI: 10.3389/fmicb.2016.02080

[…] ke and GSU1497-like genes. Whole genome information is available for only eight Geobacter strains (Table ). Eight GSU1496-like and eight GSU1497-like genes were extracted from the eight genomes using PilFind and PSI-BLAST. […]

library_books

Structures of type IV pilins from Thermus thermophilus demonstrate similarities with type II secretion system pseudopilins

2016
J Struct Biol
PMCID: 5131608
PMID: 27612581
DOI: 10.1016/j.jsb.2016.08.006

[…] We identified a cluster of type IV pilin-like genes within the T. thermophilus HB8 genome, using the program PilFind (). Type IV pilins are highly diverse in sequence, with the exception of the N-terminal helix, which is hydrophobic and contains a highly conserved Glu or Asp residue at position 5 (). PilFind […]

library_books

Genomic insights into members of the candidate phylum Hyd24 12 common in mesophilic anaerobic digesters

2016
PMCID: 5030696
PMID: 27058503
DOI: 10.1038/ismej.2016.43

[…] e with lipopolysaccharides (see ).None of the Hyd24-12 genomes encode any flagella-related proteins, suggesting limited motility. However, genes associated with type IV pili were identified using the PilFind algorithm (see ) (). These pili enable the bacteria to generate surface-associated twitching motility. This allows them to move effectively through environments that contain shear-thinning vis […]


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PilFind institution(s)
Department of Biology and the Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
PilFind funding source(s)
Supported by the National Science Foundation (MCB02-39215) and the National Institutes of Health (R01-AI05815).

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