Consensus 20040414 – Web Interface for Finding DNA and Protein Patterns

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

:: 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.

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.

inSite – Interactive Viewer for Comparing Patterns of Binding Sites across multiple Genomics Regions

inSite

:: DESCRIPTION

inSite (interactive site viewer) is a tool for interactively visualizing binding sites along multiple genomic regions. Different types of transcription factors are encoded with color with a user-defined, interactive color legend.

::DEVELOPER

Miriah Meyer & DePace Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX

:: DOWNLOAD

inSite

:: MORE INFORMATION

CODA 1.1 – Quantitative Characterization of Crossover Position Patterns along Chromosomes

CODA 1.1

:: DESCRIPTION

CODA(CrossOver Distribution Analyzer)is a software to provide easy access to powerful and appropriate statistical and computational tools to characterize CO pathways, namely by estimating two parameters: interference strength in pathway 1, and the proportion of COs formed through pathway 2 .

:: DEVELOPER

UMR Plant Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

CODA

:: MORE INFORMATION

Citation:

M. Falque, L.K. Anderson, S.M. Stack, F. Gauthier and O.C. Martin (2009).
Two types of meiotic crossovers coexist in Maize,
The Plant Cell 21: 3915-3925.

tacg 4.1.0 – Finds Short Patterns and Specific Combinations of Patterns in Biological Strings

tacg 4.1.0

:: DESCRIPTION

tacg is a command-line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms a core of the program, it has been expanded to fill more roles, sort of a ‘grep’ for DNA.

::DEVELOPER

Harry Mangalam <harry.mangalam@uci.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

tacg

:: MORE INFORMATION

Citation

tacg–a grep for DNA.
Mangalam HJ.
BMC Bioinformatics. 2002;3:8. Epub 2002 Mar 6.

PatSearch – Detection of Patterns and Structural Motifs in Nucleotide Sequences

PatSearch

:: DESCRIPTION

PatSearch is a pattern matching tool for database searching of composite motifs including regular expression patterns, secondary structure elements, nucleotide weight matrices (e.g. TRANSFAC matrices) and allowing mismatches and/or mispairings below a user-fixed threshold;

::DEVELOPER

the Research Network of Bioinformatics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.
Grillo G, Licciulli F, Liuni S, Sbisà E, Pesole G.
Nucleic Acids Res. 2003 Jul 1;31(13):3608-12.

Voting 4 – Discover Patterns, Motif, in a set of DNA sequences

Voting 4

:: DESCRIPTION

Voting is a software package that discovers common patterns, motif, in a set of DNA sequences. Voting is efficient to solve the planted (l,d) motif problem which discover a hidden length-l string motif appear in each input DNA sequence with at most d Hamming distance. Our package guarantees discovering all motifs in a short time.

::DEVELOPER

Bioinformatics Research Group of Hong Kong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Voting

:: MORE INFORMATION

Citation:

Francis Y.L. Chin and Henry C.M. Leung.
Voting Algorithms for Discovering Long Motifs (2005)
In Proceedings of Asia-Pacific Bioinformatics Conference (APBC) pages 261 – 271

PatScan – Locate Patterns in DNA or Protein FASTA files

PatScan

:: DESCRIPTION

PatScan (scan_for_matches) is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.

::DEVELOPER

Ross Overbeek (overbeek@mcs.anl.gov); David Joerg and Morgan Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

PatScan

:: MORE INFORMATION

PatMatch 1.2 – Find Patterns in Peptide and Nucleotide Sequences

PatMatch 1.2

:: DESCRIPTION

PatMatch (Pattern Matching) allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same Arabidopsis dataset as TAIR’s BLAST and FASTA programs. If you are searching for a sequence >20 bp or aa with no degenerate positions, please use BLAST or FASTA, which are much faster. Pattern Matching allows for ambiguous characters, mismatches, insertions and deletions, but does not do alignments and so is not a replacement for BLAST and FASTA Currently the maximum number of hits retrieved is 250,000 and the minimum number of input string is 3 residues.

::DEVELOPER

The Arabidopsis Information Resource

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
Perl

:: DOWNLOAD

PatMatch

:: MORE INFORMATION

Citation:

Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY.
PatMatch: a program for finding patterns in peptide and nucleotide sequences.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W262-6.