#********************************************************************************** # PIPELINE= Annotation of bacterial genome # #********************************************************************************** #================================================================================== PHASE= Upload FASTA program = upload_fasta.pl #---------------------------------------------------------------------------------- multifastafile = bacteria.fasta sequence_type = n use_quality = yes quality_file = set_quality = 13 project_name = "Bacteria_for_course" project_description = "by Arthur Gruber" sequence_source = prokaryotic_genome organism = 8888 #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= TRF program = annotation_trf.pl #---------------------------------------------------------------------------------- minimum_alignment_score = 25 matching_weight = 2 indel_penalty = 1000 indel_probability = 10 mismatch_penalty = 1000 maximum_period_size = 100 match_probability = 80 annotation_color = 000 255 000 #report_file = trf.txt output_dir = trf_dir #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== ##================================================================================== PHASE= tRNAScan program = annotation_trna.pl #---------------------------------------------------------------------------------- secondary_structure_output_file = secondary tRNA_search_model = -G standard_output_file = /dev/null annotation_color = 255 000 000 statistics_output_file = /dev/null output_dir = trna_dir command_line_options = program_path = #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Alienhunter program = annotation_alienhunter.pl #---------------------------------------------------------------------------------- output_file=alienhunter.txt output=yes output_dir=alienhunter_dir sequence_file=regions_found.fas annotation_color = 152 152 152 input_from_evidence = false #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Infernal program = annotation_infernal.pl #---------------------------------------------------------------------------------- cm_database=/usr/local/genome/databases/Rfam/Rfam.cm.1_1 output_file=infernal.txt table_file=sample.tbl rfam_ncRNA_table=/usr/local/genome/databases/Rfam/rfam_type2ncRNA_class cpus= 12 output_dir=infernal_dir annotation_color = 123 234 255 input_from_evidence = false #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== ##================================================================================== PHASE= RNAmmer program = annotation_rnammer.pl ##---------------------------------------------------------------------------------- superkingdom=bac fasta_out=yes xml_out=yes gff_out=yes hmm_out=yes output_dir=rnammer_dir program_path= input_from_evidence = false annotation_color = 254 234 255 #=================================================================================== #=================================================================================== # || # # _||_ # # \ / # # \/ # #=================================================================================== # #=================================================================================== PHASE= TransTermHP program = annotation_transterm.pl ##---------------------------------------------------------------------------------- newest_confidence_file = /usr/local/genome/transterm/expterm.dat output=yes output_dir = transterm_dir output_file = transterm.txt annotation_color = 100 100 100 input_from_evidence = false ##================================================================================== #=================================================================================== # || # # _||_ # # \ / # # \/ # #=================================================================================== #=================================================================================== PHASE= Glimmer3 program = annotation_glimmer3.pl #---------------------------------------------------------------------------------- output_file=glimmer3.txt output_dir=glimmer3_dir linear=yes trans_table = 4 min_gene_length = 130 translation_fasta_file=genes annotation_color=0 0 255 #=================================================================================== #=================================================================================== # || # # _||_ # # \ / # # \/ # #=================================================================================== #================================================================================== PHASE= RBSfinder program = annotation_rbsfinder.pl #---------------------------------------------------------------------------------- rbs_region_length= consensus_sequence= output_file=rbsfinder.txt output_dir=rbsfinder_dir program_path= annotation_color= 125 125 255 ##================================================================================== #=================================================================================== # || # # _||_ # # \ / # # \/ # #=================================================================================== # #=================================================================================== PHASE= TCDB program = annotation_tcdb.pl #----------------------------------------------------------------------------------- database=/usr/local/genome/databases/TCDB/TCDB TCDB_file=/usr/local/genome/databases/TCDB/TCDB_ID_list maximum_Evalue=1e-10 minimum_identity_percent = 50 minimum_similarity_percent = output_file=tcdb.txt output=yes output_dir=tcdb_dir program_path= blast_num_threads= 12 #=================================================================================== # #=================================================================================== # || # # _||_ # # \ / # # \/ # #=================================================================================== #================================================================================== PHASE= Phobius program = annotation_phobius.pl #---------------------------------------------------------------------------------- input_from_evidence = true graphics_output_dir = phobius_dir output = yes output_file = phobius.txt #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= TMHMM program = annotation_tmhmm.pl #---------------------------------------------------------------------------------- input_from_evidence = true converter_eps2png = true graphics_output_dir = tmhmm_dir output = yes output_file = tmhmm.txt #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= SignalP program = annotation_signalP.pl #---------------------------------------------------------------------------------- model = euk input_from_evidence = true converter_eps2png = true graphics_output_dir = signalp_dir output = yes output_file = signalp.txt #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= BlastP x nr program = annotation_blast.pl #---------------------------------------------------------------------------------- program = blastp database_code = INSD database = /usr/local/genome/databases/nr/nr input_from_evidence = true command_line_options = -num_descriptions 10 -num_alignments 10 -num_threads 20 minimum_identity_percent = 0 output = yes output_file = blastp.txt output_dir = blastp_dir annotation_color = 000 255 112 number_of_top_scoring_matches = 2 maximum_Evalue = 1e-06 minimum_block_size = 0 minimum_similarity_percent = 55 #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Motif search with RPS-BLAST program = annotation_rpsblast.pl #---------------------------------------------------------------------------------- database = /usr/local/genome/databases/cdd/Cdd input_from_evidence = true command_line_options = -num_threads 20 number_of_top_scoring_matches = 2 output = yes output_dir = rpsblast_dir maximum_Evalue = 5e-04 ##================================================================================= #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Interpro search program = annotation_interpro.pl #----------------------------------------------------------------------------------- GO_OBO_file = /usr/local/genome/databases/go/gene_ontology.obo sequence_type = protein output_file = interpro.txt output = yes output_dir = interpro_dir input_from_evidence = true program_path = command_line_options = #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= eggNOG orthology search program = annotation_orthology.pl #---------------------------------------------------------------------------------- database_code=eggnog orthology_map_file=/usr/local/genome/databases/orthology/eggMap_v4 database=/usr/local/genome/databases/orthology/eggnogv4.proteins.all.fa output_file = eggnog.txt output_dir = eggnog_dir output = yes blast_num_threads= 20 input_from_evidence=true #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= KEGG pathway mapping program = annotation_pathways.pl #---------------------------------------------------------------------------------- organism_data_set = all_orgs database_dir= /usr/local/genome/databases/kegg/genes/KEGG_fasta_database/ ko_file= /usr/local/genome/databases/kegg/ko/ko output = yes output_file = kegg.txt output_dir = kegg_dir blast_num_threads = 20 input_from_evidence=true #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Conclusions program = report_conclusion.pl #---------------------------------------------------------------------------------- #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Assign locus tag program = assign_locus_tags.pl #---------------------------------------------------------------------------------- locus_tag_prefix = Bact locus_tag_digits = 2 reassign_locus_tags=no next_locus_tag=1 #================================================================================== #================================================================================== # || # # _||_ # # \ / # # \/ # #================================================================================== #================================================================================== PHASE= Outsave program = outsave.pl #---------------------------------------------------------------------------------- savefile = bacteria.xml file_format = xml #==================================================================================