jrl%life@LANL.GOV (02/23/88)
From: jrl%life@LANL.GOV (John Lawton)
Dear Dr. McClure,
I am responding to your SEQNET bulletin board request for a list of codon
frequency. This information comes from the LiMB (LIsting of Molecular Biology
databases) database at Los Alamos Nat'l Lab. It is a directory of molecular
biology and related databases. We have no entries for codon frequency of
plants in particular, but hopefully the CUTG database will help you out.
The first set of entries is a description of the LiMB entries line by line.
The information for CUTG follows that.
We will be distributing LiMB free of charge in the next week or so. If you
would like a copy of it, please send me an e-mail message and let me know
through which medium you like to receive it 1)e-mail 2)PC floppy disk or
3)hardcopy.
Sincerely,
John Lawton, LiMB Administrator
Electronic mail address: limb@lanl.gov
Telephone: (505) 667-9455
LiMB Database
T-10, Mail Stop K710
Los Alamos National Laboratory
Los Alamos, NM 87545
U.S.A.
entry AAAAAAAA (Name of entry.)
number Number that will always be associated with a given data bank.
history History of entry.
status (tentative-know about; known-no form back; response-form returned).
res.nam Name of respondent.
res.add Address of respondent.
res.tel Telephone number of respondent (as dialed in U.S.A.)
res.net Network address of respondent.
gen.nam Name for general inquiry.
gen.add Address for general inquiry.
gen.tel Telephone number for general inquiry (as dialed in U.S.A.)
gen.net Network address for general inquiry.
con.nam Name for contributing data.
con.add Address for contributing data.
con.tel Telephone number for contributing data (as dialed in U.S.A.)
con.net Network address for contributing data.
acc.nam Name for acquiring data.
acc.add Address for acquiring data.
acc.tel Telephone number for acquiring data (as dialed in U.S.A.)
acc.net Network address for acquiring data.
name.now Name of database.
name.alt Alternative names of database.
name.bad Obsolete/incorrect names of database.
source Source of data in database.
collab.in Formal collaborators for collection of data.
collab.ou Formal collaborators for distribution of data.
funding Funding base for data bank.
citation Recent publications describing database and/or data bank.
charter Formal or informal charter of database effort.
cross Other databases to which this database is cross-referenced.
data.pri Primary data items in the database.
data.sec Secondary data items in the database.
hardware Hardware the data are maintained on.
operate Operating system hardware is run under.
dbms Software system used for maintaining data.
language Programming language used for software system.
format Format used for distributed flat text files.
software Software that is distributed with the database.
access Limitations on access to data.
update Frequency of database updates.
con.onl Can contributions be made to database on-line?
con.mag Can contributions be made to database on magnetic tape?
con.flp Can contributions be made to database on floppy disk?
con.elm Can contributions be made to database by electronic mail?
con.pap Can contributions be name to database on hardcopy?
acc.onl Is database distributed on-line?
acc.mag Is database distributed on magnetic tape?
acc.flp Is database distributed on floppy disk?
acc.elm Is database distributed on electronic mail?
acc.pap Is database distributed on hardcopy?
byt.all Number of bytes contained in the database.
byt.pri Number of bytes contained in primary data items in the database.
ent.pri Number of entries (single primary data items with associated
secondary data items) in the database.
comment -
///
entry CUTG
number 00005
history cb 01/28/87 response received from T.Ikemura
fm 04/06/87 initial entry
status response
res.nam Toshimichi Ikemura
res.add National Institute of Genetics
Mishima, Shizuoka 411
JAPAN
res.tel [011-81] 559-75-0771, ext. 355
res.net -
gen.nam Toshimichi Ikemura
gen.add National Institute of Genetics
Mishima, Shizuoka 411
JAPAN
gen.tel [011-81] 559-75-0771, ext. 355
gen.net -
con.nam Toshimichi Ikemura
con.add National Institute of Genetics
Mishima, Shizuoka 411
JAPAN
con.tel [011-81] 559-75-0771, ext. 355
con.net -
acc.nam Toshimichi Ikemura
acc.add National Institute of Genetics
Mishima, Shizuoka 411
JAPAN
acc.tel [011-81] 559-75-0771, ext. 355
acc.net -
name.now Codon Usage Tabulation from GENBANK
name.alt CUTG
name.bad -
source other database (GENBANK)
collab.in -
collab.ou -
funding National Institute of Genetics (Japan)
citation Maruyama,T., Gojobori,T., Aota,S. and Ikemura,T. (1986)
Codon usage tabulated from the GenBank genetic sequence data.
<Nucl. Acids Res.> 14, r151-r197.
charter CUTG is a tabulation of codon usages in all available genes
from GENBANK.
cross -
data.pri codon usage.
data.sec [GENBANK] cross-references.
hardware FACOM
operate OSIV/F4 MSP
dbms -
language FORTRAN
format -
software -
access no limitations
update every six months
con.onl no
con.mag yes
con.flp yes
con.elm no
con.pap yes
acc.onl no
acc.mag yes
acc.flp no
acc.elm no
acc.pap yes
byt.all 560,000
byt.pri 330,000
ent.pri 1,700
comment -