New sofware for sequence comparison : LASSAP

eric.glemet at inria.fr eric.glemet at inria.fr
Mon May 5 20:11:17 EST 1997


Keywords: sequence comparison, alignments, parallelism



This is a general annoucement of Lassap release 1.0a available at:

        http://www-rocq.inria.fr/genome

****************************************************
* LASSAP : LArge Scale Sequence compArison Package *
****************************************************

LASSAP is a new software package for sequence comparison.
LASSAP currently implements all major sequence comparison algorithms

        - Blast

        - Fasta,

        - Dynamic programming : Smith/Waterman, Needleman/Wunsch,
          K-best alignments


        - string matching (Mainly for redundancy problems)

        - pattern matching algorithms (e.g. search for PROSITE patterns).

For the time being, all algorithms in LASSAP are pairwise based.
Whatever a pairwise algorithm is used in LASSAP, it shares with
all other algorithms numerous enhancements such as:

 (i)   intra- and inter-databank comparisons
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       (a databank can be a set of sequences choosen among a large
        databank or one sequence);

 (ii)  computational requests
       ~~~~~~~~~~~~~~~~~~~~~~
       (selections and computations are achieved on the fly);

 (iii) frame translations on queries and databanks
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       (various genetic codes)

 (iv) structured results allowing easy and powerful post-analysis
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      (LASSAP provides 3 different views of a result:
        . a full ASCII form, whith the alignment.
        . a compacted ASCII, one line for a pairwise result, allowing
          easy "grep", "awk" or  "perl" filters
        . a structured form to perform some complex analysis such as
          clustering, etc.)

 (v)  performance improvements by parallelization
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      and the driving of specialized hardware.
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

     ( Two versions of LASSAP are available:
        . one sequencial for basic needs
        . one parallel to speed-up algorithms, and for  large scale
          problems.
       LASSAP implements an optimized version of Smith/Waterman algorithm
       using SUN Visual Instruction Set [2])

For a programmer point of vue, LASSAP is a programmable,
high-performance system designed to raise current  limitations of
sequence comparison programs in order to fit the needs  of large-scale
analysis. LASSAP provides an API (Application Programming Interface)
allowing the integration of any generic pairwise-based algorithm.
(The public API is not yet available, but it will be released
 as soon as possible)

________
Results:
--------

LASSAP is both an integrated software for end-users and a framework
allowing the integration and the combination of new algorithms.
LASSAP is involved in different projects such as:
     - the building of PRODOM
       (http://protein.toulouse.inra.fr),
     - the exhaustive comparison of microbial genomes
       (Protein Science, Vol 6, Suppl 1, April 1997)

     - the subfragments matching problem of TREMBL.
       (Proceedings of ISMB 97 conference - June, Greece)

A LASSAP  server will be set up soon through a collaborative project
between INRIA, INFOBIOGEN and CNUSC.
___________
References:
-----------
[1]     E. Glemet and JJ. Codani
        LASSAP, a LArge Scale Sequence compArison Package
        Cabios, Vol 13., No. 2, pp 137-143 (1997)

[2]     A. Wozniak
        Using Video Oriented Instructions to Speed-Up Sequence Comparison
        Cabios, Vol 13., No. 2, pp 145-150 (1997)

_____________
Availability:
-------------

LASSAP binaries release 1.0a are available for UNIX
platforms (SGI, Solaris, AIX, Digital, ...).

You can get documentation and binaries at the following address:

       http://www-rocq.inria.fr/genome


For any request or feed-back please mail to: lassap at inria.fr
                                         or  Eric.Glemet at inria.fr

Adress: E. Glemet and JJ. Codani
        INRIA Rocquencourt,
        Domaine de Voluceau, BP 105,
        78153 Le Chesnay Cedex, France


--
==============================================================================
Eric GLEMET                     | Email : eric.glemet at inria.fr
Institut National de Recherche  |
en Informatique et Automatique  |Phone: +33 1 39 63 50 77
B.P. 105                        |Fax:   +33 1 39 63 53 30
78153 Le chesnay Cedex          |
France                          |
==============================================================================

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