Match-Box Web Server 1.3

Christophe Lambert, Eric Depiereux and co-workers

Molecular Biology Research Unit , The University of Namur, Belgium.

Université de Namur

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  visitors since Feb 21 2001

MATCH-BOX - The Match-Box software proposes protein sequence multiple alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement: in the Match-Box method, gaps are the result of the alignment and not a governing parameter of the matching procedure. A reliability score is provided below each aligned position. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.

Ask for a free Match-Box trial software

BioXpr SA: Company providing bioinformatics services.

Data and parameters input for the Match-Box server:

Your email address
Job title (optional)

Input parameters

Scoring matrix (help) Sequences input format (help)
You can upload a sequence file

(Characters others than the standard 20 amino acids codes will be removed)

or paste your formatted sequences


Output options (help)       

Orientation of the report tables

Return alignment in:

PostScript format
FASTA format
MSF format
HSSP format


return reports in plain text format.
return log file of execution.

Match-Box FAQ subscription: (help)

Subscribe to FAQ. Unsubscribe to FAQ. Return subscribers' list.

Information about the Match-Box server:

MATCH-BOX - Simultaneous alignment of several protein sequences where each aligned position is weighted by a reliability score.

Help pages

New features

Registration form

Other lab www services

Please send comments and enquiries to:

   Prof. Eric Depiereux

   University of Namur    :   Tel: +32-81-72-44-15 
   Laboratoire BMS        :   Fax: +32-81-72-44-01
   Rue de Bruxelles, 61   :   E-mail:
   5000 Namur, Belgium    :           


Project supported by the Walloon Government , Federal State of Belgium.


  1. Depiereux, E. & Feytmans, E.
    Simultaneous and multivariate alignment of protein sequences: correspondance between physicochemical profiles and structurally conserved regions (SCR).
    Prot. Engng. 4(6):603-613 (1991)

  2. Depiereux, E. & Feytmans, E.
    MATCH-BOX - A fundamentally new algorithm for the simultaneous alignment of several protein sequences.
    Comput. Appl. Biosci. 8(5):501-509 (1992)

  3. Depiereux, E., Baudoux, G., Briffeuil, P., Reginster, I.,De Bolle, X., Vinals, C., Feytmans, E.
    Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability.
    Comput. Appl. Biosci. 13(3):249-256 (1997)

  4. Briffeuil, P., Baudoux, G., Lambert, C., De Bolle, X., Vinals, C., Feytmans, E. and Depiereux, E.
    Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance predictions reliability.
    Bioinformatics. 14(4):357-366 (1998)