Patser v3e – Find Locations of Patterns in Sequence

Patser v3e

:: DESCRIPTION

Patser scores the L-mers (subsequences of length L) of the indicated sequences against the indicated alignment or weight matrix.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CCompiler

:: DOWNLOAD

 Patser

:: MORE INFORMATION

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)

PalCheck – Online Multiple Palindrome Pattern Matching

PalCheck 1.2

:: DESCRIPTION

PalCheck is a java program that supports both online palindrome pattern matching and online multiple palindrome pattern matching.

::DEVELOPER

Theory of Computation Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 PalCheck

:: MORE INFORMATION

Citation

OMPPM: Online Multiple Palindrome Pattern Matching.
Kim H, Han YS.
Bioinformatics. 2015 Dec 16. pii: btv738.

QuasiMotiFinder v4 – Protein Annotation Using a Search for Signature Like Patterns

QuasiMotiFinder v4

:: DESCRIPTION

QuasiMotiFinder is a server for the identification of signatures and signature-like patterns in protein sequences

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W255-61.
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
Gutman R, Berezin C, Wollman R, Rosenberg Y, Ben-Tal N.

TIPR – Transcription Initiation Pattern Recognition on a Genome Scale

TIPR

:: DESCRIPTION

TIPR (Transcription Initiation Pattern Recognizer) is a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TIPR

:: MORE INFORMATION

Citation

TIPR: transcription initiation pattern recognition on a genome scale.
Morton T, Wong WK, Megraw M.
Bioinformatics. 2015 Aug 8. pii: btv464.