CRISPRmap protocols

View CRISPRmap computational protocol

CRISPRmap statistics

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CRISPRmap specifications

Information


Unique identifier OMICS_03716
Name CRISPRmap
Interface Web user interface
Restrictions to use None
Input data CRISPR sequence(s) (repeat sequence only)
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Publications for CRISPRmap

CRISPRmap in pipeline

2017
PMCID: 5398294
PMID: 28379509
DOI: 10.1093/gbe/evx062

[…] the crispr layouts reported previously (). in each crispr type, consensus sequences of all repeat sequences were determined using weblogo v3.3 (). the repeat sequences were further analyzed using crisprmap v3.1.5 to characterize their directions (). the phage-like structures in the crisprs were identified using both nucleotide sequence similarity with the reported phage sequences in the ncbi […]


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CRISPRmap in publications

 (10)
PMCID: 5704556
PMID: 29218031
DOI: 10.3389/fmicb.2017.02234

[…] structures of the dr repeat sequence were visualized using the rna fold program (ding et al., ). phylogenetic relationships of the consensus dr sequences in the dr database were analyzed using crisprmap (lange et al., ). gene neighborhoods were visualized using tools at the joint genome institute (markowitz et al., ). venn diagrams were generated using […]

PMCID: 5570325
PMID: 28837670
DOI: 10.1371/journal.pone.0183752

[…] based on the threshold of sequence identity 0.8. the obtained clusters were verified manually. for classifying each repeat cluster and predicting repeat orientation, an integrated web server (i.e., crisprmap v2.1.3–2014 and crisprstrand) was used [, ]. each repeat cluster was named with the length value of the consensus repeat sequence and the serial number within the length value as the repeat […]

PMCID: 5529391
PMID: 28798737
DOI: 10.3389/fmicb.2017.01410

[…] of which were analyzed to study the evolution and probable viral diversity respectively. classification and clustering of crispr repeats and repeat-based cas gene predictions were undertaken using crisprmap, a comprehensive cluster analysis method (based on markov clustering) which clusters conserved sequence families and potential structure motifs (lange et al., ). repeats were classified […]

PMCID: 5099237
PMID: 27877161
DOI: 10.3389/fmicb.2016.01751

[…] gap extend -2, nucleotide match +1, mismatch -1, e-value 0.1, word size 7) (). direct repeat seqences were submitted to crisprdb () and blasted against the crisprfinder database (e-value 10e-2) and crisprmap () to examine their superclasses by sequence and structure and to determine if they were reported before. the origin of the crispr arrays was determined through their respective contigs […]

PMCID: 4814470
PMID: 27064693
DOI: 10.3389/fmicb.2016.00398

[…] with default parameters for short input sequence (word size 7, gapopen 5, gapextend 2, reward 2, penalty -3, e-value 0.01). repeat sequences from identified crispr arrays were classified using crisprmap tool (lange et al., ). the cas genes search was performed using mg-rast subsystems annotation tool (meyer et al., )., to amplify crispr arrays of flavobacterium psychrophilum from total dna […]


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CRISPRmap institution(s)
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ZBSA Centre for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, Albert-Ludwigs-University Freiburg, Germany; Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark

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