|KLAST: high-performance sequence similarity search tool|
KLAST's major features:
Fast and Accurate
KLAST is a new optimized implementation of the Inria's PLAST algorithm, to which several improvements have been made.
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.).
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.
Depending on your needs and your user profile, KLAST is available from an integrated graphical workbench, ngKLAST, a graphical data analysis and workflow-based platform, KNIME, and a command-line tool, KlastRunner.
ngKLAST being a fully integrated graphical workbench, its audience targets biologists. KNIME's plugin is more oriented to the setup of custom-made workflows, and it is more adapted for bioinformaticians.
In addition to these graphical tools, KLAST is available with KlastRunner, a 100% pure command-line tool. It is more suited for computational intensive using batch job execution mode, and it is well adapted for use on clusters.
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.
KLAST provides flexibility in a variety of ways:
KLAST starter configuration is: