OAT 0.91 – Similarity Measurement Tool for Genomes

OAT 0.91

:: DESCRIPTION

OAT (Orthologous Average Nucleotide Identity Tool) uses OrthoANI to measure overall similarity between two genome sequences.

::DEVELOPER

OAT team

:: SCREENSHOTS

OAT

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 OAT

:: MORE INFORMATION

Citation:

OrthoANI: An improved algorithm and software for calculating average nucleotide identity.
Lee I, Kim YO, Park SC, Chun J.
Int J Syst Evol Microbiol. 2015 Nov 18. doi: 10.1099/ijsem.0.000760.

WormGender 20150417 – Automatic Caenorhabditis Elegans Sex Ratio Measurement

WormGender 20150417

:: DESCRIPTION

WormGender is an open-source software which designed for accurate quantification of sex ratio in Caenorhabditis elegans.

:: DEVELOPER

Zhong’s lab

:: SCREENSHOTS

WormGender

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • JRE

:: DOWNLOAD

 WormGender

:: MORE INFORMATION

Citation

WormGender – Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.
Labocha MK, Jung SK, Aleman-Meza B, Liu Z, Zhong W.
PLoS One. 2015 Sep 30;10(9):e0139724. doi: 10.1371/journal.pone.0139724.

GS-align – Glycan Structure Alignment and Similarity Measurement

GS-align

:: DESCRIPTION

GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.

::DEVELOPER

Wonpil Im Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GS-align

:: MORE INFORMATION

Citation

GS-align for Glycan Structure Alignment and Similarity Measurement.
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W.
Bioinformatics. 2015 Apr 8. pii: btv202

WaveRead – Measurement of relative Gene Expression levels from Microarrays using Wavelet analysis

WaveRead

:: DESCRIPTION

Waveread is an automated microarray quantification program based on feature detection by wavelet packet decomposition analysis. The algorithm handles rotated images (up to 45°), spot detection, meta-gridding separation, gridding, background correction, and spot irregularities.

::DEVELOPER

FCCC Bioinformatics, Fox Chase Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

  Waveread

:: MORE INFORMATION

Citation

J Biomed Inform. 2006 Aug;39(4):379-88.
WaveRead: automatic measurement of relative gene expression levels from microarrays using wavelet analysis.
Bidaut G, Manion FJ, Garcia C, Ochs MF.

targetedRetrieval 120705 – Targeted Retrieval of Gene Expression Measurements Using Regulatory Models

targetedRetrieval 120705

:: DESCRIPTION

targetedRetrieval is a model for the regulation of specific genes from a data repository and exploit it to construct a similarity metric for an information retrieval task.

::DEVELOPER

Elisabeth Georgii

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

  targetedRetrieval

:: MORE INFORMATION

Citation

Elisabeth Georgii, Jarkko Salojärvi, Mikael Brosché, Jaakko Kangasjärvi, and Samuel Kaski.
Targeted retrieval of gene expression measurements using regulatory models.
Bioinformatics (2012) 28 (18): 2349-2356.

GPODE 20090927 – Learning Gene Regulatory Networks from Gene Expression Measurements

GPODE 20090927

:: DESCRIPTION

GPODE (GP4GRN) is a software of learning the structure of gene regulatory networks using non-parametric molecular kinetics. A set of Matlab functions that implement our gene regulatory network inference method. The method can use time-series and steady state gene expression (and protein) measurements and makes Bayesian inference for the network structure using Gaussian process based non-parametric molecular kinetics

::DEVELOPER

Tarmo Äijö

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

 GPODE

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 15;25(22):2937-44. Epub 2009 Aug 25.
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.
Aijö T, Lähdesmäki H.

DSection – Probabilistic Analysis of Gene Expression Measurements from Heterogeneous Tissues

DSection

:: DESCRIPTION

DSection is a model for reconstructing cell type specific gene expression profiles from measurements of heterogeneous tissues.

DSection Online Version

::DEVELOPER

Timo Erkkilä

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

 DSection

:: MORE INFORMATION

Citation:

Probabilistic analysis of gene expression measurements from heterogeneous tissues.
Erkkilä T, Lehmusvaara S, Ruusuvuori P, Visakorpi T, Shmulevich I,Harri Lähdesmäki.
Bioinformatics. 2010 Oct 15;26(20):2571-7. Epub 2010 Jul 14.

ws2m 3.2 – Software for the Measurement and Analysis of Species Diversity

ws2m 3.2

:: DESCRIPTION

Ws2m does the job of estimating the total number of types in a finite collection. It was developed to estimate the number of species in a collection of identified individuals.

::DEVELOPER

Will Turner (wturner@u.arizona.edu), Wade Leitner, and Michael Rosenzweig

:: SCREENSHOTS

ws2m

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Ws2m

:: MORE INFORMATION