Cister protocols

Cister specifications

Information


Unique identifier OMICS_13964
Name Cister
Alternative name Cis-element Cluster Finder
Interface Web user interface
Restrictions to use None
Input data DNA sequences or a GenBank identifier, types of cis-elements, algorithmic parameters
Input format FASTA
Output data Annotated protein coding regions, a plot with cis-elements positions, a table of high-scoring cis-elements
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Martin Frith <>

Information


Unique identifier OMICS_13964
Name Cister
Alternative name Cis-element Cluster Finder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequences or a GenBank identifier, types of cis-elements, algorithmic parameters
Input format FASTA
Output data Annotated protein coding regions, a plot with cis-elements positions, a table of high-scoring cis-elements
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Martin Frith <>

Publication for Cis-element Cluster Finder

Cister IN pipelines

 (9)
2016
PMCID: 4899598
PMID: 27314006
DOI: 10.1155/2016/9543274

[…] there are a total of 1,283 positions in the final dataset. evolutionary analyses are conducted in mega6 [8]., to predict the cis-regulatory regions in dna sequences of hhvs, standalone version of cister (cis-element cluster finder) tool [9] is used. default parameters of cister tool are used along with default nucleotide count matrices for the selection of 16 cis-elements available […]

2016
PMCID: 4899598
PMID: 27314006
DOI: 10.1155/2016/9543274

[…] are a total of 1,283 positions in the final dataset. evolutionary analyses are conducted in mega6 [8]., to predict the cis-regulatory regions in dna sequences of hhvs, standalone version of cister (cis-element cluster finder) tool [9] is used. default parameters of cister tool are used along with default nucleotide count matrices for the selection of 16 cis-elements available on the given […]

2016
PMCID: 4899598
PMID: 27314006
DOI: 10.1155/2016/9543274

[…] are conducted in mega6 [8]., to predict the cis-regulatory regions in dna sequences of hhvs, standalone version of cister (cis-element cluster finder) tool [9] is used. default parameters of cister tool are used along with default nucleotide count matrices for the selection of 16 cis-elements available on the given webpage (http://zlab.bu.edu/~mfrith/nucfreqmat.html)., to determine […]

2013
PMCID: 3693062
PMID: 23805135
DOI: 10.3389/fmicb.2013.00172

[…] automated search for alternative promoters and regulatory regions in 10 kb region up and downstream of the envelope gene in the genbank reference sequence (al39009.10, position 10079 to 32008) using cister (cis-element cluster finder) (frith et al., 2001) and promoterscan (http://www-bimas.cit.nih.gov/molbio/proscan/) tools., since the herv-w envelope can work as autoantigen and hypothetically, […]

2009
PMCID: 2760101
PMID: 19844571
DOI: 10.1371/journal.pone.0007534

[…] gene-regulatory regions were identified on the basis of clustering of transcription factor (tf) dna-binding sites, as identified by the tf-search engine (www.cbrc.jp/research/db/tfsearch) and the cis-element cluster finder (cister)-program (http://zlab.bu.edu/%7emfrith/cister.shtml) using matrixes from transfac (http://www.gene-regulation.com). tfs predicted to bind proximal to snps verified […]

Cister institution(s)
Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA
Cister funding source(s)
This work was partially supported by NSF grant DBI#0078194 and by NIH grant #CA81157.

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