Match-Box Web Server 1.3 Guy Baudoux, Christophe Lambert, Ernest Feytmans and Eric Depiereux. Molecular Biology Research Unit, The University of Namur, Belgium. Project supported by the Walloon Government, Federal State of Belgium.

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NEW VERSION !

Please send comments and enquiries to:

   Dr. Eric Depiereux

   University of Namur    :   Tel: +32-81-72-44-15 
   Laboratoire BMS        :   Fax: +32-81-72-44-15  
   Rue de Bruxelles, 61   :   E-mail: matchbox-help@fundp.ac.be
   5000 Namur, Belgium    :           

QUICK START
MORE INFORMATION
REGISTRATION
REFERENCES
LEGAL NOTICE
ACKNOWLEDGEMENTS

I. QUICK START

You can send up to 50 sequences of no more than 2000 amino acids each. The name of the sequences is truncated to 10 characters.

The FREE format requires to separate each sequence by

>sequence_name

followed by a carriage return. The 10 first characters are taken as sequence name.

Only the 20 standard one letter code amino acids are recognized. Numbers will be deleted and other characters will be transformed into gaps. Embedded comments are not detected and will be treated as sequence data. Dots (".") and hyphens ("-") are interpreted as gaps.

Example:

>DHICS_DH
VGVVGTGHIVFLGQQT.IVINTARPYILNFA.....RGTLIDSEDVGIVGGNVGR
RL
RTYU*
>DLDHLAC_DE
VGVIGTGRIGRAAHIGQVYILNF--ARGTLIDSED
FLINTGRGPLVDTYE
VLSPHIAYYTE
>LDH
VGFRGFG..GGGHHHH*


FASTA, MSF and HSSP formats can also be interpreted.

If the data are not presented in these formats, unpredictable results can occur.

The default scoring matrix used is Henikoffs' BLOSUM62 (5)

As output, by default, you will receive two files:

• an "alignment" report in plain text format
• an "explore" report in plain text format.

In plain text files, aligned residues are printed in lowercase, and in the PostScript file, they are outlined. Please note that alignments must be displayed or printed with non-proportional fonts (like monaco or courier) and that big files (like PostScript files) can be cut in parts by some email clients programs.

II. MORE INFORMATION

Registration.

Input formats.

Computation performed.

Output.

Scoring matrices.

Example1 sequence data set.

Example2 sequence data set.

Example3 sequence data set.

FAQ distribution.

This server is available 10 times without registration. An application form for registration will be sent automatically to you at your last free submission, but you may use immediately the registration form. Registration is fees free.

IV. REFERENCES

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

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

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

4. Briffeuil, P., Baudoux, G., Reginster, I., Depiereux, E., Feytmans, E. (1997). Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance predictions reliability. Comp. Appl. Biosci. Accepted for publication.

5. Henikoff, S. & Henikoff, J.G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89, 10915-10919.

V. LEGAL NOTICE

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