The KLAST Extension for KNIME
knime bioinformatics metagenomics workflow sequence search alignment structure tree phylogenetic genomics proteomics Software design bioinformatic analysis biological databanks biological information systems   knime workbench sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems


Using the popular open-source KNIME workflow design interface, researchers can easily assemble individual "nodes" into a complete workflow. With the addition of the Korilog's KLAST Extension for KNIME, it is now easy to setup and run sequence comparison workflows directly within KNIME using the new KLAST high-performance sequence similarity search tool. KLAST jobs can be run using a graphical interface or from the command-line. The KLAST Extension is also ready for cluster execution.

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The KLAST Extension (release 3.5) for KNIME provides several additional nodes to setup bioinformatics workflows within the KNIME platform. All these nodes are ready to handle large set of sequences and run sequence comparison workflows in multi-threaded batch mode. Data produced with such workflows can be provided to other existing KNIME data handling nodes for further analysis and visualization.

Main Features
 Databank Installation
 Sequence Databank Manager sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems 

- Automatic deployment from remote servers
- Install public databanks (NCBI, EMBL, Uniprot,...)
- Prepare personal databanks
- Setup annotated KLAST databanks
- Manage sequences, annotations and biological classifications
- Prepare taxonomic subsets from public databanks

 Bioinformatics Workflow Design
 Knime Bioinformatics Workflow sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

- Load query sequence files
- Setup KLAST high-performance sequence similarity comparisons
- Annotate KLAST results with qualified data sets
- Annotate KLAST results with Taxonomy, Enzyme & Gene Onotology classifications
- Filter results using KLAST and/or annotation data

- View some examples of KLAST-based workflows

 Analyse and Visualize
 Knime Taxonomy Evaluation sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems

- Use Knime provided data analysis and visualization tools
- Use Knime extended data analysis nodes (e.g. "R" statistical package)
- Use Korilog data visualisation tools (e.g. KoriViewer)
- Export KLAST results and annotation in various formats (text, xml, csv, html)


Installation modes: from desktop computers to clusters, and high-performance ready

The KLAST Extension for KNIME is available for use on:

  • Desktop computers
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    Modern desktop computers usually contain 64 bits multi-cores processor running Windows 7, MacOS X or Linux. Simply use your desktop computer to run KNIME-based KLAST high-performance sequence comparisons.
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  • Cluster infrastructures
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    KNIME-based KLAST workflows are ready to be run from the command-line. This way, you'll be able to schedule KLAST jobs on your cluster system.

    Or, you can use the KLAST plugin with the Cluster Extension of KNIME. Configure your KLAST workflows and run it on your cluster in a few mouse clicks.

The Korilog/KLAST plugin is available for all releases of KNIME: Desktop, Professional, Team Space, Server and Cluster Execution.

Command-line execution is also available. It is then possible to integrate KLAST high-performance engine in your existing bioinformatics workflows, relying on personal scripts and routines. You can even integrated our framework within the well-known Galaxy platform.


System requirements

   The KLAST Extension for Knime is available for use on linuxlogo.png,maclogo.pngandwinlogo.png platforms.



Contact us to discuss with you the opportunities of using KLAST and our KNIME extension for your research works.

 
 
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