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LASSAP, a LArge Scale Sequence compArison Package

E Glémet1, J J Codani

  • 1INRIA Rocquencourt, Domaine de Voluceau, Le Chesnay, France. Eric.Glemet@inria.fr

Computer Applications in the Biosciences : CABIOS
|April 1, 1997
PubMed
Summary

LASSAP is a new software package for sequence comparison, overcoming limitations for large-scale analysis. It integrates various algorithms and offers enhanced features for efficient data processing and analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Existing sequence comparison programs face limitations for large-scale analysis.
  • There is a need for high-performance, programmable systems to address these limitations.

Purpose of the Study:

  • Introduce LASSAP, a novel software package for sequence comparison.
  • Enable integration of generic pairwise algorithms via an Application Programming Interface (API).
  • Facilitate large-scale sequence analysis with enhanced capabilities.

Main Methods:

  • LASSAP implements various sequence comparison algorithms including Fasta, Blast, and Smith/Waterman.
  • It supports intra- and inter-databank comparisons with on-the-fly computations.
  • Features include frame translations, structured results, and parallelization for performance optimization.

Main Results:

  • LASSAP provides numerous enhancements applicable to all integrated algorithms.
  • It supports efficient, on-the-fly computational requests and structured post-analysis.
  • Performance is improved through parallelization and specialized hardware utilization.

Conclusions:

  • LASSAP serves as both an end-user software and a flexible framework for integrating new algorithms.
  • It has been successfully applied in projects like PRODOM, yeast sequence comparison, and TREMBL subfragment matching.
  • LASSAP effectively addresses current limitations in sequence comparison for large-scale biological data analysis.

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