tRNA Infernal Analysis

This module will run cmscan on the user input sequence to find hits against the PtRNAdb databse infernal models of the tRNA sequences. cmscan will structurally algin the user query sequence with the tRNA infernal models selected by the user. For more details user can refer to the help page. The user can select different models according to the input sequence.

Type/paste query sequences in FASTA format:

or Upload your sequence

Select one plant name from any of the below given genome levels: Nuclear genome: Actinidia_chinensisActinidia_erianthaAegilops_tauschiiAlloteropsis_semialataAndrographis_paniculataArabidopsis_thalianaArabis_alpinaArachis_duranensisArachis_hypogaeaArachis_ipaensisArachis_monticolaAsparagus_officinalisBathycoccus_prasinosBeta_vulgarisBrachypodium_distachyonBrassica_junceaBrassica_napusBrassica_nigraBrassica_oleraceaBrassica_rapaCajanus_cajanCamelina_sativaCannabis_sativaCapsicum_annuumCapsicum_baccatumCapsicum_chinenseCenchrus_americanusCicer_arietinumCitrullus_lanatusCitrus_maximaCitrus_sinensisCoffea_arabicaCoffea_canephoraCoffea_eugenioidesCucumis_sativusCucurbita_pepoCynara_cardunculusDaucus_carotaDioscorea_rotundataElaeis_guineensisEutrema_salsugineumFagopyrum_tataricumGlycine_maxGlycine_sojaGossypioides_kirkiiGossypium_arboreumGossypium_hirsutumGossypium_raimondiiIpomoea_batatasIpomoea_trifidaIpomoea_trilobaLagenaria_sicerariaLeersia_perrieriLinum_usitatissimumLupinus_angustifoliusMalus_domesticaManihot_esculentaMedicago_truncatulaMiscanthus_sacchariflorusMorella_rubraMusa_acuminataMusa_balbisianaNelumbo_nuciferaNicotiana_attenuataOlea_europaeaOryza_barthiiOryza_brachyanthaOryza_glumipatulaOryza_longistaminataOryza_meridionalisOryza_punctataOryza_sativaOstreococcus_tauriPanicum_halliiPanicum_miliaceumPapaver_somniferumPhaseolus_vulgarisPhyscomitrella_patensPopulus_trichocarpaPrunus_persicaQuercus_lobataRaphanus_sativusRosa_chinensisSaccharum_spontaneumSchrenkiella_parvulaScutellaria_baicalensisSetaria_italicaSetaria_viridisSolanum_lycopersicumSolanum_pennelliiSorghum_bicolorSpatholobus_suberectusSpirodela_polyrhizaTheobroma_cacaoTrifolium_pratenseTriticum_aestivumTriticum_dicoccoidesTriticum_urartuUtricularia_gibbaVigna_angularisVigna_radiataVigna_unguiculataVitis_ripariaVitis_viniferaZea_maysZiziphus_jujuba   Plastidial genome: Actinidia_chinensisActinidia_erianthaAegilops_tauschiiAlloteropsis_semialataAndrographis_paniculataArabidopsis_thalianaArachis_hypogaeaAsparagus_officinalisBathycoccus_prasinosBrachypodium_distachyonBrassica_napusBrassica_nigraBrassica_oleraceaBrassica_rapaCajanus_cajanCamelina_sativaCannabis_sativaCapsicum_annuumCapsicum_baccatumCapsicum_chinenseCenchrus_americanusCicer_arietinumCitrullus_lanatusCitrus_maximaCitrus_sinensisCoffea_arabicaCoffea_canephoraCucumis_sativusCucurbita_pepoDaucus_carotaDioscorea_rotundataElaeis_guineensisEutrema_salsugineumFagopyrum_tataricumGlycine_maxGlycine_sojaGossypium_arboreumGossypium_hirsutumGossypium_raimondiiIpomoea_batatasIpomoea_trifidaIpomoea_trilobaLagenaria_sicerariaLinum_usitatissimumManihot_esculentaMedicago_truncatulaMiscanthus_sacchariflorusMorella_rubraMusa_balbisianaNelumbo_nuciferaNicotiana_attenuataOlea_europaeaOryza_barthiiOryza_brachyanthaOryza_glumipatulaOryza_longistaminataOryza_meridionalisOryza_punctataOryza_sativaOstreococcus_tauriPanicum_miliaceumPapaver_somniferumPhaseolus_vulgarisPhyscomitrella_patensPopulus_trichocarpaPrunus_persicaQuercus_lobataRaphanus_sativusRosa_chinensisSaccharum_spontaneumSchrenkiella_parvulaScutellaria_baicalensisSetaria_italicaSetaria_viridisSolanum_lycopersicumSolanum_pennelliiSorghum_bicolorSpirodela_polyrhizaTheobroma_cacaoTriticum_aestivumTriticum_urartuUtricularia_gibbaVigna_angularisVigna_radiataVigna_unguiculataVitis_ripariaVitis_viniferaZea_maysZiziphus_jujuba   Mitochondrial genome: Oryza_sativaArabidopsis_thalianaBathycoccus_prasinosBeta_vulgarisBrassica_napusBrassica_nigraBrassica_oleraceaBrassica_rapaCannabis_sativaCapsicum_annuumCitrullus_lanatusCitrus_sinensisCucumis_sativusCucurbita_pepoDaucus_carotaGlycine_maxGlycine_sojaGossypium_arboreumGossypium_hirsutumGossypium_raimondiiMalus_domesticaMedicago_truncatulaNelumbo_nuciferaNicotiana_attenuataOstreococcus_tauriPhyscomitrella_patensRaphanus_sativusRosa_chinensisSolanum_lycopersicumSolanum_pennelliiSorghum_bicolorSpirodela_polyrhizaTriticum_aestivumVigna_angularisVigna_radiataVitis_viniferaZea_maysZiziphus_jujuba

Choose either isoacceptor or isodecoder option: Select isoacceptor:  Alanine Arginine Asparagine Aspartic Acid Cysteine Glutamine Glutamic Acid Glycine Histidine Isoleucine iMethionine Leucine Lycine Methionine Phenylalanine Proline Selenocysteine Serine Suppressor Threonine Tryptophan Tyrosine Valine     Select isodecoder:  AGC CGC GGC TGC ACG CCG CCT GCG TCG TCT ATT GTT ATC GTC ACA GCA CTG TTG CTC TTC ACC CCC GCC TCC ATG GTG AAT GAT TAT CAT AAG CAA CAG GAG TAA TAG CTT TTT CAT AAA GAA AGG CGG GGG TGG TCA ACT AGA CGA GCT GGA TGA CTA TCA TTA AGT CGT GGT TGT CCA ATA GTA AAC CAC GAC TAC