Cister – Find Motif Clusters in DNA Sequences

Cister

:: DESCRIPTION

Cister (Cis-element Cluster Finder) predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Linux / SUN Solaris 8 / SGI/IRIX/ Alpha (Compaq Tru64 UNIX V5.0A)

:: DOWNLOAD

Cister

:: MORE INFORMATION

Cister Web Version

Citation

Frith, M. C., Hansen U. and Weng, Z.
Detection of cis-element clusters in higher eukaryotic DNA
Bioinformatics 2001 Oct;17(10):878-889.

COMET – Cluster Of Motifs E-value Tool

COMET

:: DESCRIPTION

COMET (Cluster Of Motifs E-value Tool) finds statistically significant clusters of motifs in a DNA sequence. The motifs are represented using 4 x L matrices, which record the frequencies of the nucleotides A, C, G, and T at each position in the motif.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Linux / SUN Solaris 8 / SGI/IRIX/ Mac OS X / Alpha (Compaq Tru64 UNIX V5.0A)

:: DOWNLOAD

COMET

:: MORE INFORMATION

COMET Web Version

Citation:

Frith MC, Spouge JL, Hansen U, Weng Z
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.
Nucleic Acids Res 2002 Jul 15;30(14):3214-24

 

Cluster-Trainer 20071204 – Estimates Optimal Motif Weights for Cluster-Buster

Cluster-Trainer 20071204

:: DESCRIPTION

Cluster-Trainer is an auxiliary program for use with Cluster-Buster. It estimates optimal ‘motif weights’ to use with Cluster-Buster. These weights can also be interpreted as abundances of the motifs (occurences per kb). Given a set of DNA sequences and a set of motif definitions, Cluster-Trainer will estimate how abundant each motif is in the sequences, and the average distance between neighboring motifs.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Cluster-Trainer ; Source Code

:: MORE INFORMATION

Comments and questions to Martin Frith

 

Cluster-Buster 20100219 – Find Dense Clusters of Motifs in Nucleotide Sequences

Cluster-Buster 20100219

:: DESCRIPTION

Cluster-Buster is the third generation program for finding clusters of pre-specified motifs in nucleotide sequences. The main application is detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Windows with CygWin / Linux / Mac OsX

:: DOWNLOAD

Cluster-Buster

:: MORE INFORMATION

Cluster-Buster Online Version

Citation:

Martin C Frith, Michael C Li, and Zhiping Weng (2003). Cluster-Buster: Finding dense clusters of motifs in DNA sequencesNucleic Acids Research, 31(13):3666-8.

 

ICSF – Identification of Conserved Structural Features

ICSF

:: DESCRIPTION

ICSF (Identification of Conserved Structural Features) is a Perl program that identifies conserved structural features at sequentially degenerate locations in transcription factor binding sites. ICSF uses base-pair step parameters obtained from a collection of high-resolution DNA crystal structures to discover structural conservation that exists in the sequentially degenerate areas within a binding site and produce profiles of the structural features along the entire site.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • Perl

:: DOWNLOAD

ICSFSupplemental Information

:: MORE INFORMATION

Burden HE, Weng Z.
Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites.
Genome Inform. 2005;16(1):49-58.

 

REPFIND 20040309 – Find Clustered, Exact Repeats in Nucleotide Sequences

REPFIND 20040309

:: DESCRIPTION

REPFIND is a program to find clustered, exact repeats in nucleotide sequences. For each repeat cluster that it finds, it calculates a P-value, which indicates the probability of finding such a concentration of that particular repeat just by chance. Of the many possible clusters for each repeated word, REPFIND selects the one with the most significant P-value.

We are using REPFIND to study localization of messenger RNAs. These molecules sometimes contain signals in their 3′ untranslated regions that specify how they are transported in the cell, prior to being translated. This process is essential for establishing body axes in embryogenesis, among other things. The localization signals often appear to consist of repeat clusters that can be detected by REPFIND.

::DEVELOPER

the Center for Advanced Genomic Technology

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

REPFIND

:: MORE INFORMATION

REPFIND Online Version

Citation:

JN Betley, MC Frith, JH Graber, S Choo, JO Deshler (2002). A ubiquitous and conserved signal for RNA localization in chordates. Current Biology, 12, 1756-61.

MOMA – Minimal Perturbation Analysis

MOMA

:: DESCRIPTION

MOMA (Minimization of Metabolic Adjustment) generates predictions of flux distribution for perturbed metabolic networks.

::DEVELOPER

Daniel Segre’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MOMA ; BioSpice MOMA

:: MORE INFORMATION

Citation:

Analysis of optimality in natural and perturbed metabolic networks
by Daniel Segre’ , Dennis Vitkup and George M. Church, Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117

Bio-SPICE Dashboard 7.0 – Viological Simulation Program for Intra- & Inter-Cellular Evaluation

Bio-SPICE Dashboard 7.0

:: DESCRIPTION

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending, and exploiting these tools to further our knowledge of biological processes.

Bio-SPICE is intended for modeling and simulation of spatio-temporal processes in living cells.

The core of the Bio-SPICE application is called the Dashboard. The Bio-SPICE Dashboard has an Update Center and allows for different tool functionality to be downloaded, data to be specified, and both to be integrated into tool chains and work flows for modeling, analysis, and simulation.

::DEVELOPER

Biospice Project Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

Bio-SPICE Dashboard ; Tutorial ; plugin modules

:: MORE INFORMATION

Bio-SPICE is now released under the open-source Bio-SPICE BSD License.

Pointillist 2.1.2 – MATLAB Codes of Iterative Framework for Biological Modeling

Pointillist 2.1.2

:: DESCRIPTION

Pointillist is a set of MATLAB codes for inferring the set of elements affected by a perturbation of a biological system, based on multiple types of evidence. The integration methods in Pointillist are general-purpose and may be applied to integrate data from any existing and future technologies without requiring training datasets.

::DEVELOPER

Computational Biology, Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Pointillist ; maunal ;  Java version

:: MORE INFORMATION

Citation:

Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H. “A data integration methodology for systems biology.” Proc Natl Acad Sci U S A 2005; 102(48) 17296-17301.

ISBJava 2.4.4 – Java library for Research in Computational Biology

ISBJava 2.4.4

:: DESCRIPTION

The ISBJava project is a library (collection) of classes written in the Java programming language, that are intended to be used for research in computational biology.

::DEVELOPER

Stephen Ramsey in the laboratory of Hamid Bolouri at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

ISBJava ; manual

:: MORE INFORMATION

The license agreement is the GNU Lesser General Public License (LGPL), which is a standard “free software” and “open source” license.

Please e-mail comments or corrections regarding this document to:  isbjava at systemsbiology.org