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

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 9.0.2 – Visualization for Genome-scale Data

IGB 9.0.2

:: 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.

SurreyFBA 1.32 – Constraint-based modeling of Genome-scale Metabolic Reaction Networks

SurreyFBA 1.32

:: DESCRIPTION

SurreyFBA  provides constraint-based simulations and network map visualization. In addition to basic simulation protocols, the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments, but not available in other commonly used programs.

::DEVELOPER

Division of Microbial Sciences, University of Surrey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 SurreyFBA

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):433-4. doi: 10.1093/bioinformatics/btq679. Epub 2010 Dec 9.
SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.
Gevorgyan A, Bushell ME, Avignone-Rossa C, Kierzek AM.

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

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

MSOAR 2.0 / MultiMSOAR 2.0 – Ortholog Assignment on Genome Scale.

MSOAR 2.0 / MultiMSOAR 2.0

:: DESCRIPTION

MSOAR may be used to perform ortholog assignment between two genomes A and B.(If two genomes have different number of chromosomes, it is required that A has more chromosomes than B).The assignment of orthologous genes between a pair of genomes is usually done using sequence similarity search. We recently proposed an ortholog assignment program (SOAR for System for Ortholog Assignment by Reversals) based on a new combinatorial approach that combines sequence similarity and genome rearrangements. Here we continue the development of this approach and unite genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, homologous gene are identified using sequence similarity search and orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangements and (post-speciation) gene duplications. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs (i.e. paralogs produced by post-speciation duplications). The approach has been implemented as a high-throughput system, called MSOAR, for genome-scale ortholog assignment.

MultiMSOAR is an acurrate identification of ortholog groups

::DEVELOPER

MSOAR team

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MSOAR , MultiMSOAR

:: MORE INFORMATION

Citation:

MSOAR 2.0: Incorporating Tandem Duplications into Ortholog Assignment Based on Genome Rearrangement
Guanqun Shi, Liqing Zhang, Tao Jiang,
In Proc. 8th LSS Computational Systems Bioinformatics Conference (CSB), Stanford, August, 2009, pp.12-24

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes.
Shi G, Peng MC, Jiang T.
PLoS One. 2011;6(6):e20892. doi: 10.1371/journal.pone.0020892.

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

PCBI/Penn Center for Bioinformatics 

:: 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

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.

Trellis / Trellis+ – Genome-scale Disk-based Suffix Tree Indexing

Trellis / Trellis+

:: DESCRIPTION

Trellis is a disk-based suffix tree indexing methods (with suffix links) that is capable of indexing the entire human genome on a commodity PC with limited memory.

Trellis+ extends Trellis by further removing some memory limitations by using a novel guide suffix tree in memory.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Trellis / Trellis+

:: MORE INFORMATION

Citation

Benjarath Phoophakdee and Mohammed J. Zaki,
Genome-scale Disk-based Suffix Tree Indexing.
In ACM SIGMOD International Conference on Management of Data. Jun 2007.

Benjarath Phoophakdee and Mohammed J. Zaki,
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences using Suffix Trees.
In 13th Pacific Symposium on Biocomputing. Jan 2008