CENSOR protocols

CENSOR specifications

Information


Unique identifier OMICS_05560
Name CENSOR
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CENSOR

CENSOR IN pipelines

 (9)
2017
PMCID: 5568218
PMID: 28832642
DOI: 10.1371/journal.pone.0182029

[…] exons using clustal w [30] in the bioedit software [31] and visual inspection. repetitive dna elements (processed pseudogenes, lines, c repeats, etc.) were identified by blast searches and with the censor software tool provided by the genetic information research institute [32]., touchdown pcr was used to amplify an 1882 bp genomic region containing the remnant δch2 and δch3 exons from iberian […]

2016
PMCID: 4977797
PMID: 27551343
DOI: 10.3897/CompCytogen.v10i2.7081

[…] (http://www.ncbi.nlm.nih.gov), as well as in the repbase database (jurka et al. 2005) from the genetic information research institute (giri) (http://www.girinst.org/repbase/), using the software censor (kohany et al. 2006)., cot1-dna libraries were tagged using digoxigenin-11-dutp for nick translation reaction, according to manufacturer’s instructions (dig-nick translation mix roche). […]

2015
PMCID: 4411706
PMID: 25928409
DOI: 10.1186/s13062-015-0055-8

[…] all sequences analyzed in our work are publicly available in genbank. protein sequences were aligned using mafft [25]. local tblastn- and blastn-based sorted searches were performed using censor [26]. phylogenetic analysis was performed using phyml with the rtrev model, a discrete gamma model with 10 categories and estimated gamma shape parameter, best of the nnis and sprs tree […]

2015
PMCID: 4494074
PMID: 26019167
DOI: 10.1093/gbe/evv100

[…] order to see their target preference or specificity. target preference for microsatellites was determined manually. target preference for multicopy genes or transposons was determined by performing censor (kohany et al. 2006) against repbase. if a certain type of sequence is seen in more than 20% of the flanking sequences of a certain non-ltr retrotransposon family, this family is considered […]

2013
PMCID: 3688939
PMID: 23824673
DOI: 10.1371/journal.pone.0066693

[…] breakpoints into specific chromosome regions, and to find out cellular genes located at or near the hpv16 integration sites. cellular repetitive sequences were identified and classified by using the censor tool [77]. the exon-intron structure of cellular genes was analyzed with the ensembl genome browser (see http://www.ensembl.org/index.html)., fisher’s exact test was used to analyze […]

CENSOR institution(s)
Genetic Information Research Institute, Mountain View, CA, USA

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