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CisPlusFinder specifications


Unique identifier OMICS_12880
Name CisPlusFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Genome sequences
Input format FASTA
Output data CisPlusFinder returns the coordinates of predicted cis-regulatory module.
Output format BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Tie-IxHash, BLAST
Maintained No



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Publication for CisPlusFinder

CisPlusFinder in publications

PMCID: 5117513
PMID: 27871221
DOI: 10.1186/s12859-016-1354-5

[…] instead, most newer programs combine phylogeny and possibly other information with tfbs patterns, either with consistent positioning (stubb []; emma []; twine []) or without it ([]; phylocon []; cisplusfinder []; cistargetx [, ]). programs searching a single genome for the consistent positional preferences within rms are therefore surprisingly rare []., notably, all our significant clusters […]

PMCID: 2996316
PMID: 21152003
DOI: 10.1371/journal.pcbi.1001020

[…] prediction methods, we selected twelve representative methods from the above four search strategies families: mscan , mcast , clusterbuster , stubb , stubbms , morphms , cismodule , multimodule , cisplusfinder , phastcons score (, regulatory potential and eel . these twelve methods cover almost all the possible combinations of crm […]

PMCID: 2395258
PMID: 18226245
DOI: 10.1186/gb-2008-9-1-r22

[…] batteries.) also, the pfrsearcher method relied crucially on inter-species comparison. another algorithm to leverage evolutionary comparisons for crm prediction (without motif knowledge) is called 'cisplusfinder', developed by pierstoff et al. []. more recently, sosinsky et al. [] have proposed a method that uses pattern discovery from seven drosophila genomes to predict crms genome-wide, […]

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CisPlusFinder institution(s)
Institute for Genetics, University of Cologne, Cologne, Germany; Faculty of Life Sciences, University of Manchester, Manchester, UK
CisPlusFinder funding source(s)
This project was supported by a Marie Curie visiting fellowship from the European Commission (HPMT-GH-01-00285-13).

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