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 <>

Cister article

Cister citations

 (2)
2016
PMCID: 4899598

[…] 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 […]

2009
PMCID: 2760101

[…] 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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