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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Robert Edgar <>

Publication for PILER-CR

library_books

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

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

PILER-CR citations

 (46)
library_books

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain Specific Genes and Resolves Metagenomics Data Down to the Strain Level

2018
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 […]

library_books

Genome based classification of micromonosporae with a focus on their biotechnological and ecological potential

2018
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 […]

library_books

Insights into origin and evolution of α proteobacterial gene transfer agents

2017
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 […]

library_books

Complete Genome Sequence of a Novel Bioflocculant Producing Strain, Microbacterium paludicola CC3

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, […]

library_books

The CRISPR Spacer Space Is Dominated by Sequences from Species Specific Mobilomes

2017
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 […]

library_books

On the Origin of Reverse Transcriptase Using CRISPR Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

2017
PMCID: 5513706
PMID: 28698278
DOI: 10.1128/mBio.00897-17

[…] spacer assembly, clustering of spacer sequences, translation of putative orfs in metagenomic contigs, and curation of blast result files., for broader metagenomic searches, the crisprfinder () and piler-cr () programs were used with default parameters to identify crispr arrays found in cas7f and tnsa/tnsd loci. the megablast program () (word size, 18; otherwise, default parameters) was used […]


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

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