Tag: DNA

IQPNNI 3.3.2 – Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data

IQPNNI 3.3.2

:: DESCRIPTION

IQPNNI (Important Quartet Puzzling and NNI Operation) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n^2) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

  IQPNNI

:: MORE INFORMATION

Citation:

Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time.
Mol. Biol. Evol., 21(8):1565-1571.

CoTrix 3.0 – Analysis of complex DNA Banding Patterns

CoTrix 3.0

:: DESCRIPTION

CoTrix is an interactive user-friendly computer programme for analysis of complex DNA banding patterns.

::DEVELOPER

Bernd Degen

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CoTrix

:: MORE INFORMATION

Citation

Degen, B.; Ziegenhagen, B.; Gillet, E.; Scholz, F., 1995:
Computer-aided search for codominant markers in complex haploid DNA banding patterns – A case study in Abies alba MILL..
Silvae Genetica 44 5-6: 274-282

FunSiP 0.8.1b – Prediction of Functional Sites in DNA

FunSiP 0.8.1b

:: DESCRIPTION

FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. FunSip is a platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in the human and Arabidopsis thaliana genome.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 FunSiP

:: MORE INFORMATION

Citation:

Van Bel, M., Saeys, Y., Van de Peer, Y. (2008)
FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA.
Bioinformatics 24, 1532-3.

MultiRNAFold 2.0 – Secondary Structure Prediction of RNA/DNA

MultiRNAFold 2.0

:: DESCRIPTION

The MultiRNAFold package contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold.

::DEVELOPER

BETA LAB – University of British Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 MultiRNAFold

:: MORE INFORMATION

Citation:

Mirela Andronescu, Zhi Chuan Zhang and Anne Condon,
“Secondary Structure Prediction of Interacting RNA Molecules“,
Journal of Molecular Biology, Vol 345/5 pp 987-1001.

Kinefold – RNA/DNA Folding Predictions

Kinefold

:: DESCRIPTION

Kinefold is a software for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints.

Kinefold Online Version

::DEVELOPER

The Isambert Lab

:: REQUIREMENTS

:: DOWNLOAD

 Kinefold

:: MORE INFORMATION

Citation:

A. Xayaphoummine, T. Bucher & H. Isambert,
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots,
Nucleic Acid Res., 33, 605-610 (2005)

ESTScan 3.03 – Detect Coding Regions in DNA/RNA Sequences

ESTScan 3.03

:: DESCRIPTION

ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.

ESTScan Online Version

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OS X

:: DOWNLOAD

 ESTScan

:: MORE INFORMATION

Citation

Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003)
Modeling sequencing errors by combining Hidden Markov models
Bioinformatics 19, ii103-ii112.

Iseli C, Jongeneel CV, Bucher P. (1999)
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.
Proc Int Conf Intell Syst Mol Biol.138-48.

BioconductorBuntu – Web-Based DNA Microarray Analysis Server

BioconductorBuntu

:: DESCRIPTION

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, and provides a user friendly web-based graphical user interface to many of the tools developed by the Bioconductor Project, whether locally or across a network. Installation is a turn-key procedure, simply based on booting off the installation CD or image file. In its current version, several microarrays analysis pipelines are supported including oligonucleotide (e.g. Affymetrix Genechips), dual or single dye (e.g. Exqion miRNA arrays) experiments, with the existing set of preprocessing methods for normalization, background correction and so on are easily expanded.

::DEVELOPER

School of Mathematics, Statistics & Applied Mathematics 
National University of Ireland Galway, University Road

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

  BioconductorBuntu iso image

:: MORE INFORMATION

Citation

Paul Geeleher, Dermot Morris, John P. Hinde and Aaron Golden
BioconductorBuntu – A Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server
Bioinformatics (2009) 25 (11): 1438-1439

BioSeqAnalyzer 1.0 – Analyze DNA and Protein Sequences

 BioSeqAnalyzer 1.0

:: DESCRIPTION

BioSeqAnalyzer is a bioinformatics software tool for analyzing DNA and protein sequences.

::DEVELOPER

Arun Jagota (biobay@comcast.net) and Jim Serwer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  BioSeqAnalyzer

:: MORE INFORMATION

Register

Genamics Expression 1.1 – DNA and Protein Sequence Analysis

Genamics Expression 1.1

:: DESCRIPTION

Genamics Expression is a revolutionary new Windows application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. The coupling of creative innovations with the very latest computing technology defines Expression as the new gold standard in computational sequence analysis.

::DEVELOPER

Genamics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Genamics Expression

:: MORE INFORMATION

If you are not a registered user of Expression, the software will expire 30 days after installation.

Align 200807 – DNA Sequence Alignment Editor

Align 200807

:: DESCRIPTION

Align is a manual DNA sequence alignment editor.

::DEVELOPER

SequentiX – Digital DNA Processing

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Align

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!