PILER-CR protocols

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PILER-CR specifications

Information


Unique identifier OMICS_03714
Name PILER-CR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.06
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Robert Edgar <>

Publication for PILER-CR

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PILER-CR: fast and accurate identification of CRISPR repeats.

2007 BMC Bioinformatics
PMCID: 1790904
PMID: 17239253
DOI: 10.1186/1471-2105-8-18

PILER-CR in pipelines

 (7)
2017
PMCID: 5244535
PMID: 28116042
DOI: 10.1186/s40793-017-0230-x

[…] procedure of the doe-jgi microbial genome annotation pipeline (mgap v.4) supported by the jgi (walnut creek, ca; usa) []. briefly, crispr elements were determined by the programs crt [] and piler-cr v1.06 []. non-coding rnas, and trnas, were predicted by trnascan-se 1.3.1 []. rrna genes were identified by hmmer 3.1b2 []. protein-coding genes were determined by prodigal v2.6.2 []. […]

2017
PMCID: 5609425
PMID: 28935746
DOI: 10.1128/genomeA.01008-17

[…] and trnascan-se version 2.0 (http://lowelab.ucsc.edu/trnascan-se/), respectively. the clustered regularly interspaced short palindromic repeat (crispr) elements were detected using piler-cr ()., one gapless circular contig was assembled, which corresponded to the chromosome of m. paludicola cc3. no plasmid sequences were detected. the chromosome was composed of 3,410,829 bp, […]

2016
PMCID: 4700575
PMID: 26734118
DOI: 10.1186/s40793-015-0121-y

[…] genome sequence is less than 1 bp in 100,000 bp., the genome was annotated automatically in genbank. in addition, we predicted cluster regularly interspaced short palindromic repeats (crisprs) with piler-cr []. we analyzed the predicted protein sequences against the national center for biotechnology information (ncbi) non-redundant database, gene ontology [], kegg [], and cog [] databases […]

2016
PMCID: 4710985
PMID: 26767091
DOI: 10.1186/s40793-015-0127-5

[…] pipeline [] and was further reviewed using the integrated microbial genomes—expert review platform []. genes were identified using prodigal []. crispr elements were detected using crt [] and piler-cr []. the final annotated genome is available from the integrated microbial genome system []., the assembly of the draft genome sequence consists of 26 scaffolds amounting to 2,748,442 bp, […]

2016
PMCID: 4715301
PMID: 26779305
DOI: 10.1186/s40793-015-0122-x

[…] peptides, crispr elements and secondary metabolite gene clusters were predicted using trnascan-se [], rnammer [], infernal [] and prokka’s prokaryotic rna covariance models [], tmhmm [], signalp [] piler-cr [] and antismash []. searching for essential genes [] was performed using hmmer3 []. ortholog detection between williamsia sp. arp1 and three other genomes were carried out with inparanoid […]


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PILER-CR in publications

 (45)
PMCID: 5797582
PMID: 29441050
DOI: 10.3389/fmicb.2018.00063

[…] annotated by their prokaryotic genome annotation pipeline version 3.3 (tatusova et al., ). putative crispr repeats (and their total number) were detected with crisprs finder (grissa et al., ) and piler-cr (edgar, ). putative cas proteins were first searched in the ncbi annotation and secondly identified using a hidden markov model (hmm) based search with hmmcas (chai et al., ). putative […]

PMCID: 5765111
PMID: 29323202
DOI: 10.1038/s41598-017-17392-0

[…] genes was determine under infernal 1.0.2. the integrated microbial genomes – expert review (img-er) platform permitted additional gene prediction analysis and functional annotation. crt and piler-cr allowed crispr element detection., the core genome was determined through the jgi tool phylogenetic profiler for single genes using the default options. crisprfinder was used to compare […]

PMCID: 5721377
PMID: 29250433
DOI: 10.1093/ve/vex036

[…] interspaced short palindromic repeats (crisprs) were identified by scanning 255 α-proteobacterial genomes for both crispr leader sequences and repeat structures using crisprleader v. 1.0.2 () and piler-cr v. 1.06 (repeat length between sixteen and sixty-four; spacer length between eight and sixty-four; minimum array length of three repeats; minimum conservation of repeats 0.9; minimum repeat […]

PMCID: 5609425
PMID: 28935746
DOI: 10.1128/genomeA.01008-17

[…] and trnascan-se version 2.0 (http://lowelab.ucsc.edu/trnascan-se/), respectively. the clustered regularly interspaced short palindromic repeat (crispr) elements were detected using piler-cr ()., one gapless circular contig was assembled, which corresponded to the chromosome of m. paludicola cc3. no plasmid sequences were detected. the chromosome was composed of 3,410,829 bp, […]

PMCID: 5605939
PMID: 28928211
DOI: 10.1128/mBio.01397-17

[…] (genome partitions, such as chromosomes and plasmids, and contigs)., all contigs from the prokaryotic genome database were analyzed with crisprfinder (), which identified 61,581 crispr arrays, and piler-cr (), which identified 49,817 arrays. arrays were merged by coordinates (crisprfinder array annotation was taken in case of overlap), which produced a set of 65,194 crispr arrays. crispr-cas […]


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PILER-CR institution(s)
45 Monterey Dr; Tiburon, CA, USA

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