CENSOR protocols

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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

 (18)
2017
PMCID: 5537241
PMID: 28761142
DOI: 10.1038/s41598-017-07231-7

[…] and blastn (detecting somewhat similar sequences). the ssusat consensus sequence was also screened against repbase, a database of representative repetitive sequences from eukaryotic species, using censor software., local blast searches against crassostrea gigas genome and partial genomic libraries of other bivalve species (donax trunculus, ruditapes decussates, and ruditapes philippinarum) […]

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

[…] igd exons using clustal w [] in the bioedit software [] 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 []., 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

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

2015
PMCID: 4320630
PMID: 25555398
DOI: 10.1186/1471-2164-16-2

[…] detect putative mitochondrial to nucleus gene transfers, a blastp (v2.2.29+) search against all mitochondrion proteins of refseq database [] was performed. also all the candidates were submitted to censor [] to detect the presence of repetitive or transposable elements., the program blast2go 2.8 [] was used to annotate the hgt candidates with gene ontology (go) terms. the annotations […]

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 () 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 target specific., […]


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CENSOR in publications

 (104)
PMCID: 5928131
PMID: 29740478
DOI: 10.3389/fgene.2018.00145

[…] 5000 bp of the contig sequence from lr-pcr was analyzed to identify two breakpoints of the gross deletion with blat using the ucsc genome browser. the known repetitive elements were evaluated by censor at the 300 nucleotide sequence flanking each breakpoint using the february 2009 human reference sequence (grch37/hg19) ()., the proband was the first child born to healthy, non-consanguineous […]

PMCID: 5874043
PMID: 29590185
DOI: 10.1371/journal.pone.0194502

[…] server [] and with the molluscan whole genomes available in ensembl metazoa (http://metazoa.ensembl.org/multi/blastview). features related to transposable elements were searched in repbase using censor (http://www.girinst.org/censor/) []. the detection of internal repeats was performed through dotlet (http://myhits.isb-sib.ch/cgi-bin/dotlet) [], while trnascan-se search server […]

PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] were included in the alignment. this process yielded three types of family: fully annotated, partially annotated and unannotated., identifiable repeat consensus sequences were annotated by using censor [] with the repbase ‘vertebrate’ library (downloaded on 1st march, 2016, includes 41,908 sequences). further annotation of consensus sequences was based on wu-blast (v2.0) […]

PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] terminal repeats and terminal inverted repeats. the \resulting consensuses were used as input for the repet annotation pipeline part, comprising the te detection software blaster, repeatmasker, and censor [–]. localizations of tes were extracted from the gff3 files, and blastn was used to find the number and size of tes in the c. cacaofunesta genome. the te consensuses and their annotated te […]

PMCID: 5786205
PMID: 29325122
DOI: 10.1093/gbe/evy008

[…] in published eukaryotic genomes were screened using approaches similar to those described previously in the literature (). screening for low-copy-number repeat sequences was also performed by censor search () with the protein sequences of well-characterized repeat sequences deposited in repbase () (http://www.girinst.org/repbase). classification is based on the similarity to known repeat […]


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

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