Tag: DNA Sequence

Miropeats 2.02 – Display DNA Sequence Similarity Information Graphically

Miropeats 2.02

:: DESCRIPTION

Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics.

::DEVELOPER

Jeremy Parsons

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Miropeats

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1995 Dec;11(6):615-9.
Miropeats: graphical DNA sequence comparisons.
Parsons JD.

PROMO – Detection of Putative Transcription Factor Binding Sites (TFBS) in DNA sequences

PROMO

:: DESCRIPTION

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files.

::DEVELOPER

the Algorithmics and Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  No

:: MORE INFORMATION

Citation

Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M.Mar Albà.
PROMO: detection of known transcription regulatory elements using species-tailored searches.
Bioinformatics, 18, 2, 333-334, 2002.

biomc2 1.9 – Detect recombination in DNA Sequence Alignments

biomc2 1.9

:: DESCRIPTION

 biomc2 is a hierarchical Bayesian procedure to detect recombination in DNA sequence alignments based on the incongruence between topologies caused by recombinational events.

::DEVELOPER

Leonardo de Oliveira Martins

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 biomc2

:: MORE INFORMATION

Citation

Leonardo de Oliveira Martins, élcio Leal and Hirohisa Kishino (2008)
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees.
PLoS ONE 3(7): e2651.

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

 

TD 2.0 – Computation of the Transformation Distance for a set of DNA sequences

TD 2.0

:: DESCRIPTION

TD (Transformation Distance) : pairwise compare sequences and reveal segment inversions, duplications.

::DEVELOPER

JS Varré, Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

 TD

:: MORE INFORMATION

Citation

JS Varré, JP Delahaye, E Rivals,
Transformation Distances: a family of dissimilarity measures based on movements of segments,
Bioinformatics, vol. 15, no. 3, pp 194-202, 1999.

Parat 0.9.1 – Estimates Site Specific Substitution Rates from a set of DNA sequences

Parat 0.9.1

:: DESCRIPTION

parat estimates site specific substitution rates from a set of DNA sequences. The rates and the phylogenetic tree relating the sequences are estimated in an iterative maximum likelihood procedure, whereby the likelihood of the inferred tree increases at each iteration step until it converges.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 parat

:: MORE INFORMATION

Citation:

S. Meyer and A. von Haeseler (2003)
Identifying site specific substitution rates.
Mol. Biol. Evol., 20, 182-189.

DNAzip – DNA Sequence Compression using a Reference Genome

DNAzip

:: DESCRIPTION

DNAzip is a series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment.

::DEVELOPER

Xiaohui Xie  and  Chen Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 DNAzip

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jan 15;25(2):274-5. Epub 2008 Nov 7.
Human genomes as email attachments.
Christley S, Lu Y, Li C, Xie X.

EulerAlign 0.9 – Alignment of DNA sequences using Eulerian graphs

EulerAlign 0.9

:: DESCRIPTION

EulerAlign is a software for alignment of DNA sequences using Eulerian graphs. The method is idea for dealing with large number of short sequences, such as many thousands sequences of 1kb long, do both global and local alignments.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EulerAlign

:: MORE INFORMATION

GenCompress 20080118 / GenDecompress – Compression / Decompression for DNA sequences

GenCompress 20080118 / GenDecompress

:: DESCRIPTION

GenCompress is an efficient compression algorithm for DNA sequences. Data compression has became a tool to retrieve information hidden in genetic sequences.

::DEVELOPER

Xin Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 GenCompress

:: MORE INFORMATION

Citation

Genome Inform Ser Workshop Genome Inform. 1999;10:51-61.
A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison.
Chen X, Kwong S, Li M.

SequenceViewer 20100606 – Viewing and Comparing DNA Sequences

SequenceViewer 20100606

:: DESCRIPTION

SequenceViewer (Sequence Viewer for Students) is an easy-to-use computer program for viewing and compare DNA sequences. The program is intended for introductory biology students with no previous genetics training.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 SequenceViewer

:: MORE INFORMATION

Citation

Kalinowski ST, MJ Leonard, TM Andrews (2010)
Sequence Viewer for Students: An easy to use computer program for viewing and comparing DNA students.
Genetics

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