3MATRIX 1.0 – Motif in 3D

3MATRIX 1.0

:: DESCRIPTION

3MATRIX visualizes the three dimensional structure of eMATRIX motifs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MATRIX motif structures. Multiple views of the structural motifs are possible.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier

:: DOWNLOAD

 3MATRIX

:: MORE INFORMATION

Citation:

Steven P. Bennett, Lin Lu, and Douglas L. Brutlag,
3matrix and 3motif: A Protein Structure Visualization System for Conserved Sequence Motifs.”
Nucleic Acids Research.

3MOTIF 2.0 – Motif in 3D

3MOTIF 2.0

:: DESCRIPTION

3MOTIF visualizes the three dimensional structure of eMOTIFs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MOTIF structures. Multiple views of the structural motifs are possible.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier

:: DOWNLOAD

 3MOTIF

:: MORE INFORMATION

Citation:

Steven P. Bennett, Craig G. Nevill-Manning, and Douglas L. Brutlag, (2003)
3motif: Visualizing Conserved Protein Sequence Motifs in the Protein Structure Database.”
Bioinformatics, Vol. 19 no. 4 2003, 541-542.

EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs

EMOTIF 3.6

:: DESCRIPTION

EMOTIF includes the following three programs:

(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.

(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.

(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier

:: DOWNLOAD

  EMOTIF

:: MORE INFORMATION

Citation:

Nevill-Manning, C. G., Wu, T. D. and Brutlag, D. L. (1998).
Highly Specific Protein Sequence Motifs for Genome Analysis.
Proc. Natl. Acad. Sci. May 26, 1998 vol. 95 no. 11 5865-5871

MotifRegressor – Find DNA Sequence Motifs

MotifRegressor

:: DESCRIPTION

MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions.

::DEVELOPER

Xiaole Shirley Liu Lab , Erin Marie Conlon 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MotifRegressor

:: MORE INFORMATION

Citation:

Conlon, E.M., Liu, X.S., Lieb, J.D., Liu, J.S. (2003)
Integrating regulatory motif discovery and genome-wide expression analysis.
Proceedings of the National Academy of Sciences USA, 100, 3339-3344.

MDScan 2004 – Find Motif from ChIP-on-chip Targets

MDScan 2004

:: DESCRIPTION

MDScan (Motif Discovery scan) discovers conserved transcription factor binding sites among upstream sequences from chromatin immune precipitation experiments (CHIP) as well as from single microarray experiments. The algorithm is strictly deterministic, not discovering local minima and always giving the globally best conserved motif. It is faster than most other algorithms and nearly as sensitive as BioProspector.

MDScan Online Version

::DEVELOPER

Xiaole Shirley Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows with Cygwin / Linux / Mac OsX
  • C Complier

:: DOWNLOAD

 MDScan

:: MORE INFORMATION

Citation:

Liu XS, Brutlag DL, Liu JS.
An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments.
Nat Biotechnol. 2002 20(8):835-9.

LocalMotif 1.0 – Discover Transcription Factor Binding Motifs

LocalMotif 1.0

:: DESCRIPTION

LocalMotif is a software tool for discovering transcription factor binding motifs in a collection of DNA sequences. LocalMotif is based on a novel scoring function, called spatial confinement score, which can determine the exact interval of localization of a motif. This score is combined with other existing scoring measures including over-representation and relative entropy to determine the overall prominence of the motif. The approach successfully discovers biologically relevant motifs and their intervals of localization in scenarios where the motifs cannot be discovered by general motif finding tools. It is especially useful for discovering multiple co-localized motifs in a set of regulatory sequences, such as those identified by ChIP-Seq.

::DEVELOPER

Dr. Sung Wing Kin, Ken.

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

LocalMotif

:: MORE INFORMATION

Citation

Narang, V., Mittal, A., Sung, W.K. (2009)
Localized motif discovery in gene regulatory sequences“,
Bioinformatics (2010) 26 (9): 1152-1159.