CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) (04/22/91)
Archive-name: bionet/molbio/genbank-codon-tables/1991-04-22 Archive-directory: frodo.mgh.harvard.edu:[.codon] [132.183.190.10] Original-posting-by: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) Original-subject: RE: codon usage Reposted-by: emv@msen.com (Edward Vielmetti, MSEN) > Has anyone assembled a codon usage table for Arabidopsis >genes? Is there much deviation from codon usage in other plants? > Eric Richards (richards@cshl.org) I have created codon usage tables for the top 47 major species represented in GenBank release 63. Within the next month I hope to update these tables. I currently available tables were produced in April 1990. You can obtain these tables via anonymous ftp from frodo.mgh.harvard.edu and iubio.bio.indiana.edu. If you don't have access to Internet you can obtain the tables from the embl-heidelberg.de mail server. You can also send me an electronic mail request. Below is a list of the higher plant tables I produced. All tables are in the GCG codon usage table format. To answer Eric's second question, I found codon usage in plants generally fell into two groups: monocots and dicots. Mike Cherry cherry@frodo.mgh.harvard.edu File Name Organism/Organelle ========== ================================= ATH.COD Arabidopsis thaliana BLY.COD Hordeum vulgare (Barley) MZE.COD Zea mays (Maize) PEA.COD Pisum sativum (Pea) PET.COD Petunia sp. PHV.COD Phaseolus vulgaris (Lima bean) POT.COD Solanum tuberosum (Potatoe) RIC.COD Oryza sativa (Rice) SOY.COD Glycine max (Soybean) TOB.COD Nicotiana tabacum (Tobacco) TOM.COD Lycopersicon esculentum (Tomato) WHT.COD Triticum aestivum (Wheat) -- comp.archives file verification frodo.mgh.harvard.edu DISK$PUBLIC2:[ANONYMOUS.CODON] ALGAE.COD;4 12 27-MAR-1991 18:50 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) ASN.COD;10 7 19-FEB-1991 11:28 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) ATH.COD;6 7 19-FEB-1991 11:28 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) BLY.COD;6 7 19-FEB-1991 11:28 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) BMO.COD;6 7 19-FEB-1991 11:30 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) BOV.COD;6 7 19-FEB-1991 11:31 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) BSU.COD;6 7 19-FEB-1991 11:32 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) CEL.COD;6 7 19-FEB-1991 11:32 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) CHI.COD;6 7 19-FEB-1991 11:33 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) CHK.COD;6 7 19-FEB-1991 11:33 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) DDI.COD;6 7 19-FEB-1991 12:04 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) DRO.COD;6 7 19-FEB-1991 12:04 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) ECO.COD;6 7 19-FEB-1991 11:34 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) HAM.COD;6 7 19-FEB-1991 11:34 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) HUM.COD;8 7 19-FEB-1991 11:35 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) KPN.COD;6 7 19-FEB-1991 11:36 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) MAC.COD;6 7 19-FEB-1991 11:36 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) MUS.COD;6 7 19-FEB-1991 11:36 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) MZE.COD;6 7 19-FEB-1991 11:36 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) MZECP.COD;6 7 19-FEB-1991 11:37 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) NEU.COD;6 7 19-FEB-1991 11:37 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) NGO.COD;6 7 19-FEB-1991 11:37 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) PEA.COD;6 7 19-FEB-1991 11:42 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) PET.COD;6 7 19-FEB-1991 11:43 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) PFA.COD;6 7 19-FEB-1991 11:43 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) PHV.COD;6 7 19-FEB-1991 11:43 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) POT.COD;7 7 21-APR-1991 23:37 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) PSE.COD;6 7 19-FEB-1991 11:56 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) RAB.COD;6 7 19-FEB-1991 11:57 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) RAT.COD;6 7 19-FEB-1991 11:58 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) READ.ME;4 4 21-APR-1991 20:21 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) RHM.COD;6 7 19-FEB-1991 11:58 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) RIC.COD;6 7 19-FEB-1991 11:58 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) SHP.COD;6 7 19-FEB-1991 11:58 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) SLM.COD;6 7 19-FEB-1991 11:59 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) SOY.COD;6 7 19-FEB-1991 11:59 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) STA.COD;6 7 19-FEB-1991 11:59 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) STY.COD;7 7 19-FEB-1991 12:00 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) SUS.COD;6 7 19-FEB-1991 12:00 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) TOB.COD;7 7 19-FEB-1991 12:00 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) TOBCP.COD;6 7 19-FEB-1991 12:01 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) TOM.COD;6 7 19-FEB-1991 12:01 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) TRB.COD;6 7 19-FEB-1991 12:01 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) WHT.COD;6 7 19-FEB-1991 12:02 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) XEL.COD;6 7 19-FEB-1991 12:02 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) YSC.COD;6 7 19-FEB-1991 12:03 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) YSCMT.COD;6 7 19-FEB-1991 12:04 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) YSP.COD;6 7 19-FEB-1991 12:04 [GUESTS,ANONYMOUS] (RWD,RWD,R,E) Total of 338 blocks in 48 files. found genbank-codon-tables ok frodo.mgh.harvard.edu:[.codon]