Tag: Query

ACIB PGDB Toolbox 1.0 – Create, Maintain and Query Pathway/Genome Databases

ACIB PGDB Toolbox 1.0

:: DESCRIPTION

ACIB PGDB Toolbox is a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface (GUI) and menu of Pathway Tools, this plug-in provides functions to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyze their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various -omics viewers of Pathway Tools

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  ACIB PGDB Toolbox

:: MORE INFORMATION

Citation

Krempl PM, Mairhofer J, Striedner G, Thallinger GG.
A Sequence Comparison and Gene Expression Data Integration Add-on for the Pathway Tools Software.
Bioinformatics. 2012 Sep 1;28(17):2283-4.

GenoPlayer 20070621 – Visualizing and Querying Genetic Data

GenoPlayer 20070621

:: DESCRIPTION

GenoPlayer is a software which is useful for visualization and manual refinement of MapPop results. Genome analysis based on molecular markers can generate large amount of information. A graphical display and visualization of the data provides a powerful overview of information and can simplify interpretation. We developed a JAVA software package, GenoPlayer, for visualizing and querying genetic linkage data. The program displays chromosomal genotypes of individuals based on molecular marker data. GenoPlayer can be used to select informative markers, to identify the most useful individuals in a segregating population, to detect segregation distortion, and to detect errors in the data.

::DEVELOPER

the Michelmore lab at UC Davis

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 GenoPlayer

:: MORE INFORMATION

GOTaxExplorer 1.0 – Tool for Querying GOTaxDB

GOTaxExplorer 1.0

:: DESCRIPTION

GOTaxExplorer, allowing for the analysis of distribution of biological processes and molecular activities over different taxonomic groups. Additionally, a functional similarity measure implemented in FSST is available for establishing functional relationships between proteins and protein families. FSST is also used by the functional similarity search in Pfam.

GOTax is a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 GOTaxExplorer

:: MORE INFORMATION

Citation:

Schlicker, A., Rahnenführer, J., Albrecht, M., Lengauer, T., Domingues, F.S. (2007)
GOTax: investigating biological processes and biochemical activities along the taxonomic tree.
Genome Biology, 8(3):R33.1-10

ARCADE 0.1 beta – Query and Visualize Data from Multiple Databases

ARCADE 0.1 beta

:: DESCRIPTION

ARCADE (A Real Time Comparative Analysis Display Environment) performs comparative queries over two or more distributed and potentially heterogeneous databases.The existence of large amounts of genomic information from many species on different databases means that sophisticated tools are required to retrieve the information important to a user and to display it a coherent manner. Furthermore, since information about one species can be used to aid research on closely related species there is great need for tools to be able to perform complex comparative queries. For example, the conserved gene order found in some cereals may be exploited to locate homologous genes in related species. ARCADE is a software tool for carrying out such comparative queries across many different sources and to display the results of these queries in a suitable coherent format.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 ARCADE

:: MORE INFORMATION

Citation:

Couchman M, Davenport G and Dicks J (2002)
A real-time comparative analysis display environment (ARCADE).
Genome Informatics, Hinxton