TS4MSBH – Tabu search algorithm for DNA Sequencing by Hybridization problem

TS4MSBH

:: DESCRIPTION

TS4MSBH is a tabu search algorithm for DNA sequencing by hybridization problem with a partial multiplicity information (a test set included)

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .NET Framework 3.5

:: DOWNLOAD

 TS4MSBH

 :: MORE INFORMATION

Tabusearch – DNA Sequencing by Hybridization with Isothermic Libraries

Tabusearch

:: DESCRIPTION

Tabusearch is a sofrware for DNA sequencing by hybridization with isothermic libraries.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Tabusearch

:: MORE INFORMATION

Citation

J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz,
Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries“,
Computational Biology and Chemistry 28, 2004, pp. 11-19.

mGenomeSubtractor 1.5 – in silico subtractive Hybridization analysis of Multiple Bacterial Genomes

mGenomeSubtractor 1.5

:: DESCRIPTION

mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions.

::DEVELOPER

Microbial Genomics and Bioinformatics Group, SKMML, SJT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W194-200. doi: 10.1093/nar/gkq326.
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.
Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z.

UNAFold 3.9-1 / mfold 3.6 / MFold Interface 1.18 – Nucleic Acid Folding & Hybridization Package

UNAFold 3.9-1 / mfold 3.6 / MFold Interface 1.18

:: DESCRIPTION

UNAFold (Unified Nucleic Acid Folding & Hybridization Package) is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature.

mfold has been replaced by UNAFold.Although UNAFold will install without mfold_util, the sir_graph and boxplot_ng programs from the mfold_util package are required in order to obtain structure plots and dot plots from UNAFold. Install mfold_util before installing UNAFold. Versions 3.4 and higher of mfold contains all of the non-interactive programs in mfold_util, so a separate download is not required.

MFold Interface is Perl/Tk GUI Interface for Dr. Michael Zuker’s MFold.

::DEVELOPER

Professor Michael Zuker  ,Wade Schulz

:: SCREENSHOTS

MFoldInterface

:: REQUIREMENTS

:: DOWNLOAD

UNAFoldmfold , MFold Interface

:: MORE INFORMATION

Citation

Methods Mol Biol. 2008;453:3-31.
UNAFold: software for nucleic acid folding and hybridization.
Markham NR, Zuker M.

FISHtrees – Phylogenetic Analysis of Multiprobe Fluorescence in situ Hybridization data

FISHtrees

:: DESCRIPTION

FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.

::DEVELOPER

FISHtrees team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FISHtrees

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Chowdhury SA1, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.

STEM 2.0 / STEM-hy 1.0 – Species Tree Estimation using Maximum likelihood (with hybridization)

STEM 2.0 / STEM-hy 1.0

:: DESCRIPTION

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 STEM / STEM-hy

:: MORE INFORMATION

Citation

Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009.
STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence,
Bioinformatics (2009) 25 (7): 971-973.doi: 10.1093/bioinformatics/btp079

OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics

OligoWalk 2

:: DESCRIPTION

OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.

::DEVELOPER

Mathews group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OligoWalk

:: MORE INFORMATION

Citation:

Efficient siRNA selection using hybridization thermodynamics
Zhi John Lu and David H. Mathews
Nucl. Acids Res. (2008) 36 (2): 640-647