NetMatchStar 3.2 – An enhanced Cytoscape network querying app

NetMatchStar 3.2

:: DESCRIPTION

NetMatch* is a Cytoscape app that allow user to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. NetMatch* also allows queries with wildcards.

::DEVELOPER

Fabio Rinnone

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

NetMatchStar

:: MORE INFORMATION

Citation

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Nov 3];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015.
NetMatchStar: an enhanced Cytoscape network querying app.
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.

Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.

Nucleosee – Visual Genome-wide search of Nucleosome Patterns

Nucleosee

:: DESCRIPTION

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Nucleosee

:: MORE INFORMATION

Citation

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192

Consensus 20040414 – Web Interface for Finding DNA and Protein Patterns

Consensus 20040414

:: DESCRIPTION

Consensus Server determines consensus patterns in unaligned sequences. The algorithm is based on a matrix representation of a consensus pattern.

::DEVELOPER

Stormo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Consensus

:: MORE INFORMATION

Citation

Bioinformatics. 1999 Jul-Aug;15(7-8):563-77.
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
Hertz GZ, Stormo GD.

Cancer3D 2.0 – Patterns of Mutations in Cancer

Cancer3D 2.0

:: DESCRIPTION

Cancer3D database provides an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins they are found in and in relation to patients gender and age.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.
Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A.
Nucleic Acids Res. 2019 Jan 8;47(D1):D895-D899. doi: 10.1093/nar/gky1098.

methylFlow – Cell-specific Methylation Pattern Reconstruction

methylFlow

:: DESCRIPTION

methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 methylFlow

:: MORE INFORMATION

Citation

methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
Dorri F, Mendelowitz L, Corrada Bravo H.
Bioinformatics. 2016 Jun 1;32(11):1618-24. doi: 10.1093/bioinformatics/btw287

Methpat 2.0.0 – A program for Summarising CpG Methylation Patterns

Methpat 2.0.0

:: DESCRIPTION

Methpat summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.

::DEVELOPER

Bernie Pope

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • Bismark v0.12.2 and it’s dependencies (bwa v0.7.5a-r405).

:: DOWNLOAD

 Methpat

:: MORE INFORMATION

Citation

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.
Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A.
BMC Bioinformatics. 2016 Feb 24;17(1):98. doi: 10.1186/s12859-016-0950-8.

SPatt 2.1 – Statistic for Patterns

SPatt 2.1

:: DESCRIPTION

SPatt is a suite of C++ programs designed for the computation of pattern occurrences p-value on text. Assuming the text is generated according to Markov model, the p-value of a given observation is its probability to occur. The lower is the p-value, the more unlikely is the observation. For example, this tools can be used to find patterns with unusual behaviour in DNA or proteins sequences.

::DEVELOPER

Gregory Nuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPatt

:: MORE INFORMATION

Citation

G. Nuel (2011).
Significance Score of Motifs in Biological Sequences.
Bioinformatics – Trends and Methodologies, Mahmood A. Mahdavi (Ed.) | www | ISBN: 978-953-307-282-1, InTech.

TPM – Temporal Pattern Mining Algorithm

TPM

:: DESCRIPTION

TPM algorithm clusters any time-series data set, specifically iTRAQ LC-MS/MS data sets. The data points that have a similar behavior over the time course are clustered together.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Fahad Saeed, Trairak Pisitkun, Mark Knepper and Jason D Hoffert,
Mining Temporal Patterns from iTRAQ Mass Spectrometry (LC-MS/MS) Data“,
The Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology (BiCoB), Vol 1. pp 152-159 New Orleans, Louisiana, USA, March 23-25, 2011 (ISBN: 978-1-880843-81-9)