Mike Cherry's codonusage database 1992 ftp://ftp.ebi.ac.uk/pub/databases/codonusage + Transterm database 1994 ftp://ftp.ebi.ac.uk/pub/databases/transterm = EMBOSS team O phage/virus (probably delete) Other sources Naming: bacteria are Egss (g=genus, ss=species) plants are 3 letter abbreviations etc. animals are common names etc. organelles are prefix ch or suffix mt/mit (make standard) Codon file Possible replacement ========== ==================== + Eacc.cut Acinetobacter_calcoaceticus O Eadenovirus5.cut Adeno-associated_virus_5 (GCG?) O Eadenovirus7.cut Adeno-associated_virus_7 (GCG?) Eaidlav.cut ******** ** identical to SV40 ** + Eanasp.cut Anabaena_sp_ + Eani.cut Emericella_nidulans (Eeni better) Eanidmit.cut mitochondrion_Emericella_nidulans + Eani_h.cut (high) # Easn.cut ******* ** Emericella nidulans or Asperguillus niger?** +# Eath.cut Arabidopsis_thaliana + Eatu.cut Agrobacterium_tumefaciens_str__C58 + Eavi.cut Azotobacter_vinelandii + Ebja.cut Bradyrhizobium_japonicum_USDA_110 +# Ebly.cut Hordeum_vulgare_subsp__vulgare (Barley) + Ebme.cut Bacillus_megaterium +# Ebmo.cut Bombyx_mori + Ebna.cut Brassica_napus # Ebov.cut Bos_taurus + Ebovsp.cut *** ** assume Bos_taurus ** + Ebst.cut Geobacillus_stearothermophilus +# Ebsu.cut Bacillus_subtilis + Ebsu_h.cut (high) + Ecac.cut Clostridium_acetobutylicum_ATCC_824 + Ecal.cut Candida_albicans + Eccr.cut Caulobacter_crescentus_CB15 +# Ecel.cut Caenorhabditis_elegans Echicken.cut *** ** assume Gallus_gallus ** # Echi.cut ??? ?? Chironomus sp. ?? + Echisp.cut ** ** assume Gallus_gallus ** # Echk.cut Gallus_gallus + Echmp.cut chloroplast_Marchantia_polymorpha + Echnt.cut chloroplast_Nicotiana_tabacum + Echos.cut chloroplast_Oryza_sativa + Echzm.cut chloroplast_Zea_mays Echzmrubp.cut *** ** single Maize chloroplast gene ** + Ecpx.cut Cyanophora_paradoxa + Ecre.cut Chlamydomonas_reinhardtii + Ecrisp.cut *** ** Cricetulus_griseus ** + Ectr.cut Chlamydia_trachomatis_D_UW-3_CX = Edayhoff.cut ... artificial ... edit ... needs stop codon frequency ... +# Eddi.cut Dictyostelium_discoideum + Eddi_h.cut (high) + Edog.cut Canis_familiaris +# Edro.cut Drosophila_melanogaster (not in species list) + Edro_h.cut (high) Edrosophila.cut *** ** Drosophila_melanogaster ** + Eeca.cut Erwinia_carotovora_subsp__atroseptica_SCRI1043. (not Equus caballus) +# Eeco.cut Escherichia_coli_K12 + Eeco_h.cut (high) Eecoli.cut *** ** Escherichia_coli_K12 ** O Ef1.cut ??? ?? phage f1 ... delete ?? Efish.cut ??? ??? fish spp or Zebrafish ?? Efmdvpolyp.cut ??? ?? foot and mouth polyprotein ?? +# Eham.cut Cricetulus_greseus (hamster) + Ehha.cut Halobacterium_salinarum_NRC-1 (Halobacterium halobium) + Ehin.cut Haemophilus_influenzae_Rd_KW20 + Ehma.cut Haloarcula_marismortui_ATCC_43049 (Halobacterium marismortui) Ehuman.cut *** ** Homo_sapiens ** +# Ehum.cut Homo_sapiens + Ekla.cut Kluyveromyces_lactis_NRRL_Y-1140 +# Ekpn.cut Klebsiella_pneumoniae + Ella.cut Lactococcus_lactis_subsp__lactis_Il1403 # Emac.cut Macaca_fascicularis Emaize.cut *** ** Zea_mays ** + Emam_h.cut (high) (Mammalian species) Emixlg.cut Emouse.cut *** ** Mus_musculus ** + Emsa.cut Medicago_sativa + Emse.cut Manduca_sexta + Emta.cut Methanothermobacter_thermautotrophicus_str__Delta_H + Emtu.cut Mycobacterium_tuberculosis_H37Rv # Emus.cut Mus_musculus + Emussp.cut *** ** Mus_musculus ** + Emva.cut ??? ?? Methanococcus vannielii ?? # Emzecp.cut *** ** chloroplast_Zea_mays (maize) ** # Emze.cut *** ** Zea_mays (maize) *** + Encr.cut Neurospora_crassa # Eneu.cut *** ** Neurospora_crassa ** # Engo.cut Neisseria_gonorrhoeae + Eoncsp.cut Oncorhynchus_mykiss (trout) + Epae.cut Pseudomonas_aeruginosa_PAO1 +# Epea.cut Pisum_sativum (pea) # Epet.cut *** ** Petunia_x_hybrida ** +# Epfa.cut Plasmodium_falciparum_3D7 O Ephix174.cut # Ephv.cut Phaseolus_vulgaris (lima bean) (Ephvu better?) + Ephy.cut Petunia_x_hybrida + Epig.cut Sus_scrofa (pig) O Epolyomaa2.cut = Epombecai.cut ... keep for chips ... maybe update ... Epombe.cut *** ** Schizosaccharomyces_pombe ** +# Epot.cut Solanum_tuberosum (potato Estu better) + Eppu.cut Pseudomonas_putida_KT2440 # Epse.cut *** ** Pseudomonas spp. *** + Epsy.cut Pseudomonas_syringae_pv__tomato_str__DC3000 + Epvu.cut Proteus_vulgaris. Erabbit.cut *** ** Oryctolagus_cuniculus (rabbit) ** # Erab.cut Oryctolagus_cuniculus (rabbit Eocu better) + Erabsp.cut *** ** Oryctolagus_cuniculus (rabbit) ** # Erat.cut Rattus_norvegicus (Erno better) + Eratsp.cut *** ** Rattus_norvegicus ** + Erca.cut Rhodobacter_capsulatus # Erhm.cut *** ** Sinorhizobium_meliloti_1021 ** +# Eric.cut Oryza_sativa (rice) (Eosa better?) + Erle.cut Rhizobium_leguminosarum + Erme.cut Sinorhizobium_meliloti_1021 + Ersp.cut Rhodobacter_sphaeroides + Esalsp.cut Salmo_salar (Atlantic salmon) (Essa better) + Esau.cut Staphylococcus_aureus + Esco.cut Streptomyces_coelicolor_A3_2_ + Esgi.cut ??? ?? Streptomyces_griseus ?? # Eshp.cut Ovis_aries (sheep Eoar better) + Eshpsp.cut *** ** Ovis_aries (sheep) ** + Esli.cut ??? ?? Streptomyces_lividans ??? # Eslm.cut ??? ?? Physarum_polycephalum slime mould ?? + Esma.cut Serratia_marcescens + Esmi.cut Schistosoma_mansoni + Esmu.cut Streptococcus_mutans_UA159 +# Esoy.cut Glycine_max (soybean Egma better) + Espi.cut Spinacia_oleracea (spinach Esol better)) + Espn.cut Streptococcus_pneumoniae_R6 + Espo.cut Schizosaccharomyces_pombe + Espo_h.cut (high) (use for CAI?) + Espu.cut Strongylocentrotus_purpuratus (sea urchin) # Esta.cut *** ** Staphylococcus_aureus ** +# Esty.cut Salmonella_typhimurium_LT2 # Esus.cut *** ** Strongylocentrotus_purpuratus (sea urchin) ** O Esv40.cut + Esyhsp.cut Synechocystis_sp__PCC_6803 + Esynsp.cut Synechococcus_sp__WH_8102 + Etbr.cut Trypanosoma_brucei + Etcr.cut Trypanosoma_cruzi + Eter.cut Thermus_thermophilus_HB8 (Ethth.cut better?) + Etetsp.cut Tetrahymena_thermophila (Eteth.cut better) # Etobcp.cut *** ** chloroplast_Nicotiana_tabacum ** +# Etob.cut Nicotiana_tabacum (tobacco Enta better) +# Etom.cut Lycopersicon_esculentum (tomato Eles better)) # Etrb.cut *** ** Trypanosoma_brucei ** + Evco.cut Vibrio_cholerae_O1_biovar_eltor_str__N16961 (Evch better) +# Ewht.cut Triticum_aestivum (wheat Etae better) +# Exel.cut Xenopus_laevis Exenopus.cut *** ** Xenopus_laevis ** = Eyeastcai.cut ... keep and annotate ... Eyeast.cut Saccharomyces_cerevisiae + Eyen.cut Yersinia_enterocolitica +# Eysc.cut *** ** Saccharomyces_cerevisiae ** + Eysc_h.cut (high) # Eyscmt.cut mitochondrion_Saccharomyces_cerevisiae # Eysp.cut *** ** Schizosaccharomyces_pombe ** Ezebrafish.cut Danio_rerio (Edre.cut better) + Ezma.cut Zea_mays Missing species from the large CUTG files: Shigella flexneri Yersinia pestis ... lots of complete genomes ...