KLAST: high-performance sequence similarity search tool

KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

     

Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

 

KLAST's major features for next-generation sequence data analysis

KLAST is a general purpose sequence comparison tool providing the following benefits.

  • KLAST is the professional version of the high-performance Parallel Local Sequence Alignment Search Tool published in BMC Bioinformatics,

  • Reduces the processing time of sequences comparisons (up to 25 times faster than Blast) while providing highest quality results,

  • Designed to compare two large sets of sequence databanks in a single run,

  • Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.)

  • Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective and takes full advantage of multi-core processors,

  • Provides an integrated algorithm suite which automatically processes analysis workflows that includes similarity searches, hits annotations, and data filtering.

 

Fast and accurate sequence similarity search tool

KLAST is fully designed to compare query and subject comprised of large sets of DNA, RNA and protein sequences using KLASTn, KLASTp, KLASTx, tKLASTx and tKLASTn methods.

KLAST is significantly faster than original PLAST, while providing comparable sensitivity to BLAST and SSearch algorithms.

KLAST contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.).

Read more about the KLAST algorithm.


KLAST has been benchmarked by the French National Center for Sequencing (Genoscope /CEA) to study metagenomics data from the Tara Oceans International Project. Read more about this analysis.

Here is an additional KLAST vs. BLAST banchmark: comparison of 2327 proteins from the black cottonwood Populus trichocarpa species against 2.9 million proteins of NCBI RefSeq databank. Both algorithms ran on an Apple MacPro computer (8 cores). Data accuracy was evaluated by comparing exact alignments obtained by each algorithm against data produced by SSearch used as the reference.

Klast speedup over Blast      Klast and Blast selectivity vs. SSearch

More about this benchmarck.

 

Integrated bioinformatics software suites

Depending on your needs and your user profile, KLAST is available from an integrated graphical workbench, ngKLAST, a workflow-based platform, KNIME, a command-line tool, KlastRunner, and CLC bio Workbenches.

 ngKLAST sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems    KLAST sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems    KLAST sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems
  KLAST for CLC bio Main and Genomics Workbenches - sequence search alignment structure tree phylogenetic bioinformatics genomics proteomics Software design bioinformatic analysis biological databanks biological information systems  

 

ngKLAST being a fully integrated graphical workbench, its audience targets biologists. KNIME's plugin is more oriented to the setup of custom-made data analytics workflows (statistical and data mining analysis).

In addition to these graphical tools, KLAST is available with KlastRunner, a 100% pure command-line tool. It is more suited for computational intensive work using batch job execution mode, and it is well adapted for use on clusters.

Flexible

KLAST does not need to use any particular data format: it directly reads FASTA sequence files for the query and the subject databanks. However, ngKLAST and KLAST's plugin for KNIME come with a Databank Manager capable of preparing sequence sets from both public and personal data sets.

Korilog Databank Manager for Knime

KLAST provides flexibility in a variety of ways:

  • Hardware: KLAST takes full advantage of Intel 64-bit multi-core processors.

  • Operating System: KLAST requires a 64-bit operating system and works on Windows 7+, Linux and MacOS X.

  • Software availability: depending on your needs and your user profile, KLAST is available from an integrated graphical workbench, ngKLAST, a workflow-based platform, KNIME, a command-line tool, KlastRunner, and CLC bio Workbenches.

  • IT Infrastructure: KLAST can be installed on a single desktop computer or on a cluster. It can be integrated within any existing sequence data analysis frameworks, including the Galaxy Platform.

  • Customization (using KNIME): as KLAST is designed for KNIME, you can create workflows integrating KLAST features, KNIME data analysis methods and your own methods in a very straightforward way.

Practical use cases of KLAST for next-generation sequence data analysis (NGS)

  KLAST can be used for:

> metagenomics, microbial communities analysis. Read more about the applications of KLAST for metagenomics analysis
> full genome & proteome comparisons
> microarray reannotations
> taxonomy & phylogenetic analyses
> pathways explorations
> functional & structural studies of proteins
> public and personal databanks management

System requirements

KLAST starter configuration is:

  • desktop computer
  • Intel or AMD 64-bit quad-core
  • 8 Gb RAM
  • Windows 7, Linux or MacOS X (64-bit required)
  • Java Runtime 1.6 (64-bit required)

Availability

KLAST is available from an integrated graphical workbench, ngKLAST, a workflow-based platform, KNIME, a command-line tool, KlastRunner, and CLC bio Workbenches.

 

KLAST product sheetDownload a product sheet

 
Some of our users:
  • tamu
  • queens
  • cirad
  • csu
  • dal
  • ijm
  • hhu
  • ifremer
  • roscoff
  • woods-hole
  • inserm
  • anderson
  • lbbe
  • pasteur
  • inra
  • canterbury
  • nebraska
  • loria
  • halle
  • lmge

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