I am very pleased to announce
CodonTree
release 1.1
Description:
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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
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Sabino Liuni
==============================================
Dr. Sabino LIUNI Area di Ricerca CNR
Administrator for the Via Amendola 166/5
Italian EMBnet Node 70126 Bari (Italy)
tel. +39-80-5482176/5482130
Fax. +39-80-5484467
E_mail:sabino at area.ba.cnr.it
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OPEN YOUR EYES TO THE WORLD OF BIOCOMPUTING
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