CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems - Test2 - elhamkhani - TriplyDB

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

http://www.wikidata.org/entity/Q28679191

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Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes Bioinformatics of prokaryotic RNAs Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data.A locus encoding variable defence systems against invading DNA identified in Streptococcus suis.An updated evolutionary classification of CRISPR-Cas systems.GraphProt: modeling binding preferences of RNA-binding proteins.CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography.Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity.Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems.Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls.CRISPRDetect: A flexible algorithm to define CRISPR arrays.Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6.Involvement of eukaryotic small RNA pathways in host defense and viral pathogenesis Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins.Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species.Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes.A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases.CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules.Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles.Cas6 processes tight and relaxed repeat RNA via multiple mechanisms: A hypothesis.The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101.CRISPRdigger: detecting CRISPRs with better direct repeat annotations Characterizing leader sequences of CRISPR loci.Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system.A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family.CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome.Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs.Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes.

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CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

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Nucleic Acids Research

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Dominic Rose

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Omer S Alkhnbashi

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Sebastian Will

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Sita J Lange

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A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.

CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein

Identification and classification of conserved RNA secondary structures in the human genome

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

A benchmark of multiple sequence alignment programs upon structural RNAs.

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

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8034-44

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1606382

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10.1093/NAR/GKT606

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17

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41

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249997033

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23863837

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3783184

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