1# tRNAscan-SE 2.0 2# Configuration File 3 4# default paths 5bin_dir: @bindir@ 6lib_dir: @libdir@/tRNAscan-SE 7infernal_dir: {bin_dir} 8 9# temporary files 10temp_dir: /tmp 11tmp_raw: {temp_dir}/tscan$$.raw 12tmp_fa: {temp_dir}/tscan$$.fa 13tmp_trnaseq_file: {temp_dir}/tscan$$.trna 14tmp_masked_fa: {temp_dir}/tscan$$.masked.fa 15 16# sequence process 17really_big_number: 1000000000 18upstream_len: 70 19downstream_len: 70 20 21# default search mode 22cm_mode: infernal 23# default cutoff bit score for infernal running as first pass scanner 24infernal_fp_cutoff: 10 25# default cutoff score for reporting of tRNA 26cm_cutoff: 20 27# default cutoff score for reporting of tRNA in organelles 28organelle_cm_cutoff: 15 29isotype_cm_cutoff.euk: 20 30isotype_cm_cutoff.arch: 20 31isotype_cm_cutoff.bact: 20 32 33# max size of -w parameter passed to covels when using a pre-scanner (eufind or tRNAscan) 34max_tRNA_length: 500 35# max size of -w param if only Cove is being used (too slow otherwise) 36max_cove_tRNA_length: 250 37# max size of -w param if only cmsearch is being used 38max_cmsearch_tRNA_length: 250 39# min length for average tRNA with no intron 40min_tRNA_no_intron: 70 41# min size of introns detected by parsing of coves output 42min_intron_length: 3 43# Below this score, tRNAs are checked for min primary and secondary structure 44# scores to catch pseudogene repeats like rat ID & rodent B2 elements 45min_cove_pseudo_filter_score: 55 46# Below this score, tRNAs are checked for min primary and secondary structure 47# scores to catch pseudogene repeats like rat ID & rodent B2 elements 48min_cmsearch_pseudo_filter_score: 55 49# Below this secondary structure score, tRNA is considered a pseudogene 50min_ss_score: 5 51# Below this primary structure score, tRNA is considered a pseudogene 52min_hmm_score: 10 53 54# legacy mode default searching parameters 55# Intermediate score cutoff for use with eufindtRNA 56eufind.intscore: -32.10 57eufind.orig_intscore: -31.25 58eufind.bact_intscore: -36.0 59eufind.arch_intscore: -36.0 60eufind.strict_param: -s 61# relaxed params to be used with eufindtRNA program by default 62eufind.relaxed_param: -r 63tscan.strict_param: -s 64tscan.relaxed_param: -r 65tscan.alt_param: -a 66 67# default cutoff score for rescanning non-canonical introns 68nci_scan_cutoff: 70 69# default score for considering non-canonical intron 70BHB_cm_cutoff: 6.5 71# default cutoff score for rescanning split tRNA 72split_tRNA_scan_cutoff: 38 73# default cutoff score for half tRNA 74half_tRNA_cutoff: 15 75left_splicing_len: 27 76right_splicing_len: 28 77 78# alternate genetic code 79gc_yeast_mito: {lib_dir}/gcode/gcode.ystmito 80gc_vert_mito: {lib_dir}/gcode/gcode.vertmito 81gc_invert_mito: {lib_dir}/gcode/gcode.invmito 82gc_ciliate_cyto: {lib_dir}/gcode/gcode.cilnuc 83gc_echinoderm_mito: {lib_dir}/gcode/gcode.echdmito 84gc_other_mito: {lib_dir}/gcode/gcode.othmito 85 86# Infernal 1.1 covariance models 87cm_dir: {lib_dir}/models 88cm.general: {cm_dir}/TRNAinf.cm 89cm.general-ns: {cm_dir}/TRNAinf-ns.cm 90cm.general1415: {cm_dir}/TRNAinf-1415.cm 91cm.general1415-ns: {cm_dir}/TRNAinf-1415-ns.cm 92cm.eukaryota: {cm_dir}/TRNAinf-euk.cm 93cm.eukaryota-ns: {cm_dir}/TRNAinf-euk-ns.cm 94cm.archaea: {cm_dir}/TRNAinf-arch.cm 95cm.archaea-ns: {cm_dir}/TRNAinf-arch-ns.cm 96cm.bacteria: {cm_dir}/TRNAinf-bact.cm 97cm.bacteria-ns: {cm_dir}/TRNAinf-bact-ns.cm 98cm.arch_5h: {cm_dir}/TRNAinf-arch-5h.cm 99cm.arch_3h: {cm_dir}/TRNAinf-arch-3h.cm 100 101# COVE covariance models 102cove_cm_dir: {lib_dir}/models 103cove_cm.general: {cove_cm_dir}/TRNA2.cm 104cove_cm.general-ns: {cove_cm_dir}/TRNA2ns.cm 105cove_cm.eukaryota: {cove_cm_dir}/TRNA2-euk.cm 106cove_cm.eukaryota-ns: {cove_cm_dir}/TRNA2-eukns.cm 107cove_cm.archaea: {cove_cm_dir}/TRNA2-arch.cm 108cove_cm.archaea-ns: {cove_cm_dir}/TRNA2-archns.cm 109cove_cm.bacteria: {cove_cm_dir}/TRNA2-bact.cm 110cove_cm.bacteria-ns: {cove_cm_dir}/TRNA2-bactns.cm 111cove_cm.ESELC: {cove_cm_dir}/ESELC.cm 112cove_cm.PSELC: {cove_cm_dir}/PSELC.cm 113 114# Isotype-specific model db 115isotype_cm_dir: {lib_dir}/models 116isotype_cm.eukaryota: {isotype_cm_dir}/TRNAinf-euk-iso 117isotype_cm.bacteria: {isotype_cm_dir}/TRNAinf-bact-iso 118isotype_cm.archaea: {isotype_cm_dir}/TRNAinf-arch-iso 119 120# tRNA-SeC models 121euk_cm.SeC: {isotype_cm_dir}/TRNAinf-euk-SeC.cm 122bact_cm.SeC: {isotype_cm_dir}/TRNAinf-bact-SeC.cm 123arch_cm.SeC: {isotype_cm_dir}/TRNAinf-arch-SeC.cm 124 125# Non-canonical intron models 126nci_cm.cren: {cm_dir}/Cren-eury-BHB-noncan.cm 127nci_cm.thaum: {cm_dir}/Thaum-BHB-noncan.cm 128 129# Mito-tRNA model db 130mito_cm_db_dir: {lib_dir}/models 131mito_cm.mammal: {mito_cm_db_dir}/TRNAinf-mito-mammal 132mito_cm.vert: {mito_cm_db_dir}/TRNAinf-mito-vert 133 134# Mammalian mito-tRNA models 135mito_cm_mammal_dir: {lib_dir}/models 136mito_cm_mammal.Ala: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Ala.cm 137mito_cm_mammal.Arg: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Arg.cm 138mito_cm_mammal.Asn: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Asn.cm 139mito_cm_mammal.Asp: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Asp.cm 140mito_cm_mammal.Cys: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Cys.cm 141mito_cm_mammal.Gln: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Gln.cm 142mito_cm_mammal.Glu: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Glu.cm 143mito_cm_mammal.Gly: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Gly.cm 144mito_cm_mammal.His: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-His.cm 145mito_cm_mammal.Ile: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Ile.cm 146mito_cm_mammal.LeuTAA: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-LeuTAA.cm 147mito_cm_mammal.LeuTAG: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-LeuTAG.cm 148mito_cm_mammal.Lys: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Lys.cm 149mito_cm_mammal.Met: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Met.cm 150mito_cm_mammal.Phe: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Phe.cm 151mito_cm_mammal.Pro: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Pro.cm 152mito_cm_mammal.SerGCT: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-SerGCT.cm 153mito_cm_mammal.SerTGA: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-SerTGA.cm 154mito_cm_mammal.Thr: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Thr.cm 155mito_cm_mammal.Trp: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Trp.cm 156mito_cm_mammal.Tyr: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Tyr.cm 157mito_cm_mammal.Val: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Val.cm 158 159# Vertebrate mito-tRNA models 160mito_cm_vert_dir: {lib_dir}/models 161mito_cm_vert.Ala: {mito_cm_vert_dir}/TRNAinf-mito-vert-Ala.cm 162mito_cm_vert.Arg: {mito_cm_vert_dir}/TRNAinf-mito-vert-Arg.cm 163mito_cm_vert.Asn: {mito_cm_vert_dir}/TRNAinf-mito-vert-Asn.cm 164mito_cm_vert.Asp: {mito_cm_vert_dir}/TRNAinf-mito-vert-Asp.cm 165mito_cm_vert.Cys: {mito_cm_vert_dir}/TRNAinf-mito-vert-Cys.cm 166mito_cm_vert.Gln: {mito_cm_vert_dir}/TRNAinf-mito-vert-Gln.cm 167mito_cm_vert.Glu: {mito_cm_vert_dir}/TRNAinf-mito-vert-Glu.cm 168mito_cm_vert.Gly: {mito_cm_vert_dir}/TRNAinf-mito-vert-Gly.cm 169mito_cm_vert.His: {mito_cm_vert_dir}/TRNAinf-mito-vert-His.cm 170mito_cm_vert.Ile: {mito_cm_vert_dir}/TRNAinf-mito-vert-Ile.cm 171mito_cm_vert.LeuTAA: {mito_cm_vert_dir}/TRNAinf-mito-vert-LeuTAA.cm 172mito_cm_vert.LeuTAG: {mito_cm_vert_dir}/TRNAinf-mito-vert-LeuTAG.cm 173mito_cm_vert.Lys: {mito_cm_vert_dir}/TRNAinf-mito-vert-Lys.cm 174mito_cm_vert.Met: {mito_cm_vert_dir}/TRNAinf-mito-vert-Met.cm 175mito_cm_vert.Phe: {mito_cm_vert_dir}/TRNAinf-mito-vert-Phe.cm 176mito_cm_vert.Pro: {mito_cm_vert_dir}/TRNAinf-mito-vert-Pro.cm 177mito_cm_vert.SerGCT: {mito_cm_vert_dir}/TRNAinf-mito-vert-SerGCT.cm 178mito_cm_vert.SerTGA: {mito_cm_vert_dir}/TRNAinf-mito-vert-SerTGA.cm 179mito_cm_vert.Thr: {mito_cm_vert_dir}/TRNAinf-mito-vert-Thr.cm 180mito_cm_vert.Trp: {mito_cm_vert_dir}/TRNAinf-mito-vert-Trp.cm 181mito_cm_vert.Tyr: {mito_cm_vert_dir}/TRNAinf-mito-vert-Tyr.cm 182mito_cm_vert.Val: {mito_cm_vert_dir}/TRNAinf-mito-vert-Val.cm 183 184# to be used for sprinzl position alignment 185# sprinzl_cm_dir: {lib_dir}/models 186# sprinzl_cm.euk: {sprinzl_cm_dir}/euk_sprinzl.cm 187# sprinzl_cm.arch: {sprinzl_cm_dir}/arch_sprinzl.cm 188# sprinzl_cm.bact: {sprinzl_cm_dir}/bact_sprinzl.cm 189 190# alternate covariance models 191# To be used in place of default models 192# Example: 193# alt_cm_dir: /tmp 194# alt_cm.Ala: {alt_cm_dir}/Ala.cm 195# alt_cm.Arg: {alt_cm_dir}/Arg.cm 196