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CCTop specifications

Information


Unique identifier OMICS_12279
Name CCTop
Alternative name CRISPR/Cas9 target online predictor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Sequence of nucleotides
Input format (Multi)fasta file
Output data The sequence of the target sites, their coordinates and their detailed information
Output format .fasta, .bed and .xls
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
Bowtie 1, bx-Python
Maintained Yes

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Maintainer


  • person_outline Juan L. Mateo

Information


Unique identifier OMICS_12279
Name CCTop
Alternative name CRISPR/Cas9 target online predictor
Interface Web user interface
Restrictions to use None
Input data Sequence of nucleotides
Input format Either single query or batch search (FASTA)
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Juan L. Mateo

Publication for CRISPR/Cas9 target online predictor

CCTop citations

 (39)
library_books

Germ cells in the teleost fish medaka have an inherent feminizing effect

2018
PLoS Genet
PMCID: 5875746
PMID: 29596424
DOI: 10.1371/journal.pgen.1007259

[…] and non-transgenic medaka. each mutant allele was identified in f1 adult fish using the primer sets shown in and sequence analysis., crispr/cas9 target sites in meioc and dazl were searched using crispr/cas9 target online predictor (cctop, http://crispr.cos.uni-heidelberg.de/) []. selected targets sites are shown in and figs and . a designed pair of oligonucleotides (50 μm each) […]

library_books

Long noncoding RNA PANDAR blocks CDKN1A gene transcription by competitive interaction with p53 protein in gastric cancer

2018
PMCID: 5833854
PMID: 29416011
DOI: 10.1038/s41419-017-0246-6

[…] single guide rna scaffold. the oligos were designed based on the target site sequence and were flanked on the 3′ end by a 3 bp ngg pam sequence. the sgrna sequence for pandar was designed using the cctop-crispr/cas9 target online predictor (http://crispr.cos.uni-heidelberg.de/index.html). the sgrna sequences for tp53 and cdkn1a were designed using e-crisp-version 5.2 website […]

library_books

Serum exosomes can restore cellular function in vitro and be used for diagnosis in dysferlinopathy

2018
Theranostics
PMCID: 5835933
PMID: 29507617
DOI: 10.7150/thno.22856

[…] were transfected with sgrna-expressing lentivirus for 12 h, followed by 0.5 µg/ml puromycin selection for 2 weeks. sgrnas targeting human dysferlin gene exons 22 and 55 were designed with the crispr/cas9 target online predictor (crispr.cos.uni-heidelberg.de, university of heidelberg, germany). the human dysferlin gene exon 22 and exon 55 target sgrna sequences […]

library_books

Identification and characterization of sodium and chloride dependent gamma aminobutyric acid (GABA) transporters from eukaryotic pathogens as a potential drug target

2018
Bioinformation
PMCID: 5818639
PMID: 29497256
DOI: 10.6026/97320630014021

[…] []. solubility status of the proteins was computed using proso []. prediction of transmembrane helices was done by tmhmm server v. 2.0 (http://www.cbs.dtu.dk/services/tmhmm/) and validated using cctop webtool (http://cctop.enzim.ttk.mta.hu/?=/jobs/submit) []. after which the 2 d format of the cctop transmembrane helices images were obtained. an in-silico prediction of protein crystallization […]

library_books

Advances in Engineering the Fly Genome with the CRISPR Cas System

2017
Genetics
PMCID: 5753851
PMID: 29301946
DOI: 10.1534/genetics.117.1113

[…] nig-fly flycas9: shigen.nig.ac.jp/fly/nigfly/cas9, - repository of cas9 and transgenic grnas fly strains and related molecular reagents; protocols, online programs for target identification, cctop: crispr.cos.uni-heidelberg.de, chopchop: chopchop.cbu.uib.no, crispor: crispor.tefor.net/, crispr optimal target finder: tools.flycrispr.molbio.wisc.edu/targetfinder, crisprscan: […]

library_books

Unlinking the methylome pattern from nucleotide sequence, revealed by large scale in vivo genome engineering and methylome editing in medaka fish

2017
PLoS Genet
PMCID: 5755920
PMID: 29267279
DOI: 10.1371/journal.pgen.1007123

[…] (method 5 in ). the hypomds, chr17:6415960–6416269 (locus 1) and chr21:25260707–25262742 (locus 2), were randomly chosen as targets for editing. sgrnas targeting these regions were designed using cctop []. the six top-ranked guide sequence designs (sets f5-01 and f5-02, for the two loci, respectively) were synthesized (thermo fisher scientific) and in vitro transcribed (method 5 in ). […]


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CCTop institution(s)
Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
CCTop funding source(s)
Supported by the European Research Council and the German Research Foundation (DFG: SFB873)

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