Announcement: Codontree Release 1.0

Sabino Liuni sabino at area.ba.cnr.it
Sat Feb 1 14:53:23 EST 1997


                        ------------------------
                              CodonTree
                              release 1.0
                       --------------------------

Description:
------------
The classic triplet code responsible for the translation  of a  mRNA  sequence
into the amino acid sequence of a protein was the first deciphered code of the
genetic language.  Owing to the  degeneration of the  genetic code,  different 
triplets (codon families) can code for the same  amino acid.  As soon  as  the 
first nucleotide sequences were produced, it was immediately clear that for  a
given gene the usage of different synonymous codons was not random but  rather
species specific, and  also  linked to its  expression and/or to  the  genetic 
compartment where it was located.

The algorithm   CODONTREE   has  been  devised    in order to  investigate the
linguistic properties of coding regions, that is, their codon strategy.
CODONTREE is able to determine:

 1) codon usage table for a set of protein coding genes;
 2) gene relationship on the basis of codon usage similarity;
 3) compositional features of protein coding genes (e.g.  base composition  at
    various codon positions).

CODONTREE works  both on a  GCG environment and on a GCG independent platform.
It has been  compiled and  tested  using DEC Alpha AXP C compiler, Borland C++
4.0    compiler, and, moreover, it is portable over any machine with an ANSI C 
standard compiler.

The recognized formats of the input sequences are:
 - in GCG environment     FASTA/Pearson | GCG Flat File     | 
			  GCG DB Entry  | Multi GCG (@list)
 - in NoGCG environment   FASTA/Pearson.   

CODONTREE program and documentation are available on anonymous ftp:
	 address:    area.ba.cnr.it   (193.205.35.100)
         path:       pub/embnet/software/Codontree

For support and any information contact:
	Sandra Brunetta:  areasb16 at area.ba.cnr.it
	Sabino Liuni:     sabino at area.ba.cnr.it

-------------
Sabino Liuni


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