CUTG: Codon Usage Tabulated from GenBank README (Updated Feb 18 1998)

      Originally developed by

      IKEMURA Toshimichi (tikemura@lab.nig.ac.jp)
      Professor of Division of Evolutionary Genetics
      National Institute of Genetics, 1111 Yata
      Mishima, Shizuoka 411-8540, JAPAN


      Currently programed and mainteined by

      NAKAMURA Yasukazu (ynakamu@kazusa.or.jp)
      Researcher of Laboratory of Gene Structure 2
      Kazusa DNA Research Institute, 1532-3 Yana,
      Kisarazu, Chiba 292-0812, JAPAN


Codon  usage  in  individual  genes  has  been  calculated  using  the
nucleotide sequence  data obtained from  the GenBank  Genetic Sequence
Database.   The compilation  of codon usage is  synchronized with each
major release of GenBank.


* SOURCE AND METHODS

  Compiled from NCBI-GenBank Flat File Release 104.0 [15 Dec 1997].

  Compiled sequence files are, pri1 and pri2 (primate sequence
entries), rod (rodent sequence entries), mam (other mammalian sequence
entries), vrt (other vertebrate sequence entries), inv (invertebrate
sequence entries), pln (plant sequence entries), bct (bacterial
sequence entries), vrl (viral sequence entries) and phg (phage
sequence entries).

  Other sequence files are not compiled: files for est (EST: expressed
sequence tag sequence entries),  pat  (patent sequence  entries),  rna
(Structural  RNA  sequence entries), sts  (STS:  sequence  tagged site
sequence entries), syn (synthetic and chimeric sequence entries),  una
(unanotated  sequence   entries)  and  gss   (genome  survey  sequence
entries).

  In selecting  protein  coding sequences we relied  on  the  FEATURES
tables  of  GenBank. Only complete  genes were  used  in the analysis.
Codons containing ambiguous  base (such as N) were excluded  from  the
compilation.   In GenBank,  a group of consecutive  genes whose entire
region had been sequenced were registered under one  LOCUS  name.   To
distinguish the  different  genes belonging  to  a  single  LOCUS, the
symbol  #  followed by  a  number is  added after  the LOCUS name; the
numbers  represent  the order of the  CDS registered  in the  FEATURES
table of GenBank.


* FILES

  Files  of  the  present database are  available here.   Files  named
gb***.codon list the codon use in each gene registered in the selected
GenBank Flat  Files.  The LOCUS names  given in GenBank were  used  to
designate individual genes.  Each LOCUS name is  followed by fields of
information extracted from FEATURES of each CDS for defining each open
reading frames analyzed here.  The order of the codons in the table is
the same as in the previous compilation (see the CODON_LABEL file).

  To reveal  the  characteristics  of codon  use of  a  wide  range of
organisms,  as  well as  viruses and  organella,  the  frequency  (per
thousand) of codon use in  each organism was calculated  by summing up
numbers  of codon used.   Files named  gb***.spsum  list  the  sum  of
numbers of codon use in  each species as well as viruses and organella
(see the SPSUM_LABEL file).

  The files are distributed in two forms.  One form is gzip-compressed
tar archive, the other form is as flat files.  CUTG.**.tar.gz (** is a
number  which  shows  GenBank  major  release  used  in  construction)
contains two "LABEL" files, and all of "codon" and "spsum" files.  Use
"gunzip" and "tar" to extract files  from the archive.  If you  do not
have "gunzip" and "tar"  in your  local operating system,  you can get
each file as flat text files from this directory.


* DISTRIBUTION

  Complete form of the database is available from following three URLs:

  1) DDBJ (DNA Data Bank of Japan,
        National Institute of Genetics, Mishima Japan)
  ftp://ftp.nig.ac.jp/pub/db/codon/current/

  2) DISC (DNA Information and Stock Center,
        National Institute of Agrobiological Resources, Tsukuba, Japan)
  ftp://ftp.dna.affrc.go.jp/pub/codon/current/

  3) EBI (European Bioinformatics Institute, Cambridge, UK)
  ftp://ftp.ebi.ac.uk/pub/databases/cutg/


* RELATED SERVICE ON WWW

  If you need not all data, but want to obtain codon usage tables  for
small number of species, use Codon Usage Database WWW service.  A user
can  display a  codon  usage table by searching with the Latin name of
the organisms or clicking on an anchor for alphabetical lists.

  http://www.dna.affrc.go.jp/~nakamura/codon.html


* ACCESS FOR MAINTENER

  Any requests or commnets?  Send an E-mail to ynakamu@kazusa.or.jp.


* ACKNOWLEDGMENT

  We  wish  to  thank Dr. Y. Ugawa at the  DNA  Information and  Stock
Center,  National  Institute  of  Agrobiological Resources for help in
constructing and distributing the database.  This work was suported by
a grait-in-aid for  databases from the Ministry of Education, Science,
Sports and Culture  of Japan.  Y.N. is  supported  by the  Kazusa  DNA
Research Institute Foundation.


* PLEASE CITE

Nakamura, Y., Gojobori, T. and Ikemura, T. (1997)
Codon usage tabulated from the international DNA sequence databases.
Nucl. Acids Res. 25, 244-245.
.