Codon Usage Tables

[francis at NCBI.NLM.NIH.GOV]

From: gbs at ncgr.org ("Gautam B. Singh, Ph.D.") asks:

> >I am looking for the latest codon usage or frequency tables for HUMANS.
> >Can someone please point me to the direction of a Web-site or a journal
> >that carries and periodically upadtes this information.

Bernard Bellon Universite Aix-Marseille I (France) 
(bellon at abil.univ-mrs.fr) replies:

> look at The Genetic Codes (NCBI)
> http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c

I think that although the above site has useful genetic code
information, the type of site Gautam wanted is something like that
present on:

http://www.dna.affrc.go.jp/~nakamura/   (all organisms)

or:

http://www.dna.affrc.go.jp/nakamura-bin/showcodon.cgi?species=Homo+sapiens+[gbpri]

which I append below.

best regards,

f.

--
| B.F. Francis Ouellette  
| GenBank
|
| francis at ncbi.nlm.nih.gov   



Homo sapiens [gbpri]: 9143 CDS's (4309972 codons) 

fields: [triplet] [frequency: per thousand] ([number]) 


UUU 16.2( 69983)  UCU 14.0( 60482)  UAU 12.3( 53021)  UGU  9.5( 41101)
UUC 21.4( 92168)  UCC 17.7( 76339)  UAC 17.0( 73425)  UGC 12.8( 55147)
UUA  6.3( 27078)  UCA 10.7( 46295)  UAA  0.7(  2845)  UGA  1.2(  5301)
UUG 11.5( 49424)  UCG  4.4( 18820)  UAG  0.5(  2105)  UGG 13.4( 57706)

CUU 11.6( 50193)  CCU 16.6( 71709)  CAU  9.6( 41566)  CGU  4.6( 19889)
CUC 19.5( 84206)  CCC 20.0( 86140)  CAC 14.6( 62871)  CGC 11.0( 47304)
CUA  6.3( 27292)  CCA 16.2( 69854)  CAA 11.4( 49219)  CGA  5.9( 25477)
CUG 40.5(174644)  CCG  6.9( 29575)  CAG 33.5(144372)  CGG 11.2( 48193)

AUU 15.8( 67991)  ACU 12.8( 55058)  AAU 16.6( 71645)  AGU 11.1( 47943)
AUC 23.7(102025)  ACC 21.2( 91212)  AAC 21.1( 91136)  AGC 19.1( 82311)
AUA  6.7( 29020)  ACA 14.8( 63666)  AAA 23.3(100375)  AGA 10.8( 46544)
AUG 22.6( 97396)  ACG  6.7( 28709)  AAG 34.0(146389)  AGG 10.9( 47012)

GUU 10.7( 46012)  GCU 18.7( 80498)  GAU 22.0( 94835)  GGU 11.2( 48114)
GUC 15.6( 67441)  GCC 29.1(125484)  GAC 27.0(116181)  GGC 24.0(103239)
GUA  6.6( 28395)  GCA 15.3( 65971)  GAA 27.9(120135)  GGA 16.9( 72878)
GUG 30.0(129344)  GCG  7.5( 32237)  GAG 40.6(175036)  GGG 16.7( 71996)


Coding GC 52.92% 1st letter GC 55.92% 2nd letter GC 42.28% 3rd letter GC 60.55%