Tag: Genome-scale

OrthoMCL 2.0.9 – Genome-scale Algorithm for Grouping Orthologous Protein Sequences

OrthoMCL 2.0.9

:: DESCRIPTION

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph.

::DEVELOPER

OrthoMCL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • perl
  • BLAST
  • MySql

:: DOWNLOAD

 OrthoMCL

:: MORE INFORMATION

Citation

Li Li, Christian J. Stoeckert, Jr., and David S. Roos
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Genome Res. 2003 13: 2178-2189

optGpSampler 1.1 – Sampling Constraint-based Genome-scale Metabolic Networks

optGpSampler 1.1

:: DESCRIPTION

OptGpSampler is a parallel implementation of the Artificial Centering Hit-and-Run algorithm. With this tool, you can efficiently sample the steady-state solution space of a metabolic network.

::DEVELOPER

optGpSampler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • MatLab
  • Python

:: DOWNLOAD

  optGpSampler

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 14;9(2):e86587. doi: 10.1371/journal.pone.0086587. eCollection 2014.
optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks.
Megchelenbrink W, Huynen M, Marchiori E

SIFTER 2.1.1 – Genome-scale Phylogenetic Function Annotation of Protein Families

SIFTER 2.1.1

:: DESCRIPTION

SIFTER (Statistical Inference of Function Through Evolutionary Relationships) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. SIFTER allows annotations to be made on a genomic scale.

::DEVELOPER

SIFTER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 SIFTER

:: MORE INFORMATION

Citation:

B.E. Engelhardt, M.I. Jordan, J.R. Srouji, and S.E. Brenner (2010).
Genome-scale phylogenetic function annotation of large and diverse protein families
Genome Res. 2011 July 22, 2011, doi:10.1101/gr.104687.109

SECOM 1.0 – Genome-scale Protein Domain Identification

SECOM 1.0

:: DESCRIPTION

SECOM is a rapid and sensitive genome-scale protein domain identification method.

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SECOM

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e39475. doi: 10.1371/journal.pone.0039475. Epub 2012 Jun 28.
SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification.
Fan M1, Wong KC, Ryu T, Ravasi T, Gao X.

IGB 9.1.6 – Visualization for Genome-scale Data

IGB 9.1.6

:: DESCRIPTION

IGB (Integrated Genome Browser) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.

::DEVELOPER

IGB team Department of Bioinformatics and Genomics, University of North Carolina at Charlotte

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

IGB

:: MORE INFORMATION

Citation:

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Bioinformatics. 2009 Oct 15;25(20):2730-1.

LAST r992 – Genome-Scale Sequence Comparison

LAST r992

:: DESCRIPTION

LAST enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.LAST is similar to BLAST, but it copes better with giga-scale biological sequences. It can also use sequence quality data, and it can indicate the ambiguity of each column in an alignment.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 LAST

:: MORE INFORMATION

Citation

Adaptive seeds tame genomic sequence comparison.
SM Kielbasa, R Wan, K Sato, P Horton, MC Frith,
Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110

Acorn 0.3 – Visualation of Genome Scale Metabolic Reaction Networks

Acorn 0.3

:: DESCRIPTION

Acorn go to the Models tab to see the list of the genome scale metabolic reaction networks available. Different versions of the same model represent metabolism under different nutritional conditions.

::DEVELOPER

Division of Microbial Sciences, University of Surrey

:: SCREENSHOTS

acorn

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 Acorn

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 24;12:196. doi: 10.1186/1471-2105-12-196.
Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.
Sroka J, Bieniasz-Krzywiec L, Gwóźdź S, Leniowski D, Lącki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM.