CREATE TABLE `CAFE_gene_family` ( `cafe_gene_family_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `root_id` int(10) unsigned NOT NULL, `lca_id` int(10) unsigned NOT NULL, `gene_tree_root_id` int(10) unsigned NOT NULL, `pvalue_avg` double(5,4) DEFAULT NULL, `lambdas` varchar(100) DEFAULT NULL, PRIMARY KEY (`cafe_gene_family_id`), KEY `lca_id` (`lca_id`), KEY `root_id` (`root_id`), KEY `gene_tree_root_id` (`gene_tree_root_id`) ) ENGINE=MyISAM AUTO_INCREMENT=100000103 DEFAULT CHARSET=latin1; CREATE TABLE `CAFE_species_gene` ( `cafe_gene_family_id` int(10) unsigned NOT NULL, `node_id` int(10) unsigned NOT NULL, `n_members` int(4) unsigned NOT NULL, `pvalue` double(5,4) DEFAULT NULL, PRIMARY KEY (`cafe_gene_family_id`,`node_id`), KEY `node_id` (`node_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `conservation_score` ( `genomic_align_block_id` bigint(20) unsigned NOT NULL, `window_size` smallint(5) unsigned NOT NULL, `position` int(10) unsigned NOT NULL, `expected_score` blob DEFAULT NULL, `diff_score` blob DEFAULT NULL, KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841; CREATE TABLE `constrained_element` ( `constrained_element_id` bigint(20) unsigned NOT NULL, `dnafrag_id` bigint(20) unsigned NOT NULL, `dnafrag_start` int(12) unsigned NOT NULL, `dnafrag_end` int(12) unsigned NOT NULL, `dnafrag_strand` int(2) NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL, `p_value` double NOT NULL DEFAULT 0, `score` double NOT NULL DEFAULT 0, KEY `dnafrag_id` (`dnafrag_id`), KEY `constrained_element_id_idx` (`constrained_element_id`), KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `dnafrag` ( `dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `length` int(11) NOT NULL DEFAULT 0, `name` varchar(255) NOT NULL DEFAULT '', `genome_db_id` int(10) unsigned NOT NULL, `coord_system_name` varchar(40) NOT NULL DEFAULT '', `cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC', `is_reference` tinyint(1) NOT NULL DEFAULT 1, `codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT 1, PRIMARY KEY (`dnafrag_id`), UNIQUE KEY `name` (`genome_db_id`,`name`) ) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1; CREATE TABLE `dnafrag_region` ( `synteny_region_id` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0, `dnafrag_start` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_end` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0, KEY `synteny` (`synteny_region_id`,`dnafrag_id`), KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `exon_boundaries` ( `gene_member_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned NOT NULL, `dnafrag_start` int(11) NOT NULL, `dnafrag_end` int(11) NOT NULL, `sequence_length` int(10) unsigned NOT NULL, `left_over` tinyint(1) NOT NULL DEFAULT 0, KEY `seq_member_id` (`seq_member_id`), KEY `gene_member_id` (`gene_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `external_db` ( `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `db_name` varchar(100) NOT NULL, `db_release` varchar(255) DEFAULT NULL, `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL, `priority` int(11) NOT NULL, `db_display_name` varchar(255) DEFAULT NULL, `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL, `secondary_db_name` varchar(255) DEFAULT NULL, `secondary_db_table` varchar(255) DEFAULT NULL, `description` text DEFAULT NULL, PRIMARY KEY (`external_db_id`), UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `family` ( `family_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `stable_id` varchar(40) NOT NULL, `version` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL, `description` text DEFAULT NULL, `description_score` double DEFAULT NULL, PRIMARY KEY (`family_id`), UNIQUE KEY `stable_id` (`stable_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`), KEY `description` (`description`(255)) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `family_member` ( `family_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned NOT NULL, `cigar_line` mediumtext DEFAULT NULL, PRIMARY KEY (`family_id`,`seq_member_id`), KEY `seq_member_id` (`seq_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_align` ( `gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `seq_type` varchar(40) DEFAULT NULL, `aln_method` varchar(40) NOT NULL DEFAULT '', `aln_length` int(10) NOT NULL DEFAULT 0, PRIMARY KEY (`gene_align_id`) ) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1; CREATE TABLE `gene_align_member` ( `gene_align_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned NOT NULL, `cigar_line` mediumtext DEFAULT NULL, PRIMARY KEY (`gene_align_id`,`seq_member_id`), KEY `seq_member_id` (`seq_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_member` ( `gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `stable_id` varchar(128) NOT NULL, `version` int(10) DEFAULT 0, `source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL, `taxon_id` int(10) unsigned NOT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL, `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group','current_notdumped','notcurrent') NOT NULL DEFAULT 'coding', `canonical_member_id` int(10) unsigned DEFAULT NULL, `description` text DEFAULT NULL, `dnafrag_id` bigint(20) unsigned DEFAULT NULL, `dnafrag_start` int(10) DEFAULT NULL, `dnafrag_end` int(10) DEFAULT NULL, `dnafrag_strand` tinyint(4) DEFAULT NULL, `display_label` varchar(128) DEFAULT NULL, PRIMARY KEY (`gene_member_id`), UNIQUE KEY `stable_id` (`stable_id`), KEY `taxon_id` (`taxon_id`), KEY `genome_db_id` (`genome_db_id`), KEY `source_name` (`source_name`), KEY `canonical_member_id` (`canonical_member_id`), KEY `dnafrag_id_start` (`dnafrag_id`,`dnafrag_start`), KEY `dnafrag_id_end` (`dnafrag_id`,`dnafrag_end`), KEY `biotype_dnafrag_id_start_end` (`biotype_group`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`), KEY `genome_db_id_biotype` (`genome_db_id`,`biotype_group`) ) ENGINE=MyISAM AUTO_INCREMENT=100281325 DEFAULT CHARSET=latin1 MAX_ROWS=100000000; CREATE TABLE `gene_member_hom_stats` ( `gene_member_id` int(10) unsigned NOT NULL, `collection` varchar(40) NOT NULL, `families` int(10) unsigned NOT NULL DEFAULT 0, `gene_trees` tinyint(1) unsigned NOT NULL DEFAULT 0, `gene_gain_loss_trees` tinyint(1) unsigned NOT NULL DEFAULT 0, `orthologues` int(10) unsigned NOT NULL DEFAULT 0, `paralogues` int(10) unsigned NOT NULL DEFAULT 0, `homoeologues` int(10) unsigned NOT NULL DEFAULT 0, PRIMARY KEY (`gene_member_id`,`collection`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_member_qc` ( `gene_member_stable_id` varchar(128) NOT NULL, `genome_db_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned DEFAULT NULL, `n_species` int(11) DEFAULT NULL, `n_orth` int(11) DEFAULT NULL, `avg_cov` float DEFAULT NULL, `status` varchar(50) NOT NULL, KEY `genome_db_id` (`genome_db_id`), KEY `gene_member_stable_id` (`gene_member_stable_id`), KEY `seq_member_id` (`seq_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_node` ( `node_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `parent_id` int(10) unsigned DEFAULT NULL, `root_id` int(10) unsigned DEFAULT NULL, `left_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT 0, `distance_to_parent` double NOT NULL DEFAULT 1, `seq_member_id` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`node_id`), KEY `parent_id` (`parent_id`), KEY `seq_member_id` (`seq_member_id`), KEY `root_id_left_index` (`root_id`,`left_index`) ) ENGINE=MyISAM AUTO_INCREMENT=100462681 DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_node_attr` ( `node_id` int(10) unsigned NOT NULL, `node_type` enum('duplication','dubious','speciation','sub-speciation','gene_split') DEFAULT NULL, `species_tree_node_id` int(10) unsigned DEFAULT NULL, `bootstrap` tinyint(3) unsigned DEFAULT NULL, `duplication_confidence_score` double(5,4) DEFAULT NULL, PRIMARY KEY (`node_id`), KEY `species_tree_node_id` (`species_tree_node_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_node_tag` ( `node_id` int(10) unsigned NOT NULL, `tag` varchar(50) NOT NULL, `value` mediumtext NOT NULL, KEY `node_id_tag` (`node_id`,`tag`), KEY `tag` (`tag`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_object_store` ( `root_id` int(10) unsigned NOT NULL, `data_label` varchar(255) NOT NULL, `compressed_data` mediumblob NOT NULL, PRIMARY KEY (`root_id`,`data_label`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_root` ( `root_id` int(10) unsigned NOT NULL, `member_type` enum('protein','ncrna') NOT NULL, `tree_type` enum('clusterset','supertree','tree') NOT NULL, `clusterset_id` varchar(20) NOT NULL DEFAULT 'default', `method_link_species_set_id` int(10) unsigned NOT NULL, `species_tree_root_id` int(10) unsigned DEFAULT NULL, `gene_align_id` int(10) unsigned DEFAULT NULL, `ref_root_id` int(10) unsigned DEFAULT NULL, `stable_id` varchar(40) DEFAULT NULL, `version` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`root_id`), UNIQUE KEY `stable_id` (`stable_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`), KEY `gene_align_id` (`gene_align_id`), KEY `ref_root_id` (`ref_root_id`), KEY `tree_type` (`tree_type`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_root_attr` ( `root_id` int(10) unsigned NOT NULL, `aln_after_filter_length` int(10) unsigned DEFAULT NULL, `aln_length` int(10) unsigned DEFAULT NULL, `aln_num_residues` int(10) unsigned DEFAULT NULL, `aln_percent_identity` float DEFAULT NULL, `best_fit_model_family` varchar(10) DEFAULT NULL, `best_fit_model_parameter` varchar(5) DEFAULT NULL, `gene_count` int(10) unsigned DEFAULT NULL, `k_score` float DEFAULT NULL, `k_score_rank` int(10) unsigned DEFAULT NULL, `mcoffee_scores_gene_align_id` int(10) unsigned DEFAULT NULL, `aln_n_removed_columns` int(10) unsigned DEFAULT NULL, `aln_num_of_patterns` int(10) unsigned DEFAULT NULL, `aln_shrinking_factor` float DEFAULT NULL, `spec_count` int(10) unsigned DEFAULT NULL, `tree_max_branch` float DEFAULT NULL, `tree_max_length` float DEFAULT NULL, `tree_num_dup_nodes` int(10) unsigned DEFAULT NULL, `tree_num_leaves` int(10) unsigned DEFAULT NULL, `tree_num_spec_nodes` int(10) unsigned DEFAULT NULL, `lca_node_id` int(10) unsigned DEFAULT NULL, `taxonomic_coverage` float DEFAULT NULL, `ratio_species_genes` float DEFAULT NULL, `model_name` varchar(40) DEFAULT NULL, PRIMARY KEY (`root_id`), KEY `lca_node_id` (`lca_node_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `gene_tree_root_tag` ( `root_id` int(10) unsigned NOT NULL, `tag` varchar(255) DEFAULT NULL, `value` mediumtext NOT NULL, KEY `root_id_tag` (`root_id`,`tag`), KEY `tag` (`tag`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `genome_db` ( `genome_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `taxon_id` int(10) unsigned DEFAULT NULL, `name` varchar(128) NOT NULL DEFAULT '', `assembly` varchar(100) NOT NULL DEFAULT '', `genebuild` varchar(100) NOT NULL DEFAULT '', `has_karyotype` tinyint(1) NOT NULL DEFAULT 0, `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT 0, `genome_component` varchar(5) DEFAULT NULL, `strain_name` varchar(40) DEFAULT NULL, `display_name` varchar(255) DEFAULT NULL, `locator` varchar(400) DEFAULT NULL, `first_release` smallint(6) DEFAULT NULL, `last_release` smallint(6) DEFAULT NULL, PRIMARY KEY (`genome_db_id`), UNIQUE KEY `name` (`name`,`assembly`,`genome_component`), KEY `taxon_id` (`taxon_id`) ) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1; CREATE TABLE `genomic_align` ( `genomic_align_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `genomic_align_block_id` bigint(20) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0, `dnafrag_start` int(10) NOT NULL DEFAULT 0, `dnafrag_end` int(10) NOT NULL DEFAULT 0, `dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0, `cigar_line` mediumtext NOT NULL, `visible` tinyint(2) unsigned NOT NULL DEFAULT 1, `node_id` bigint(20) unsigned DEFAULT NULL, PRIMARY KEY (`genomic_align_id`), KEY `genomic_align_block_id` (`genomic_align_block_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`), KEY `dnafrag` (`dnafrag_id`,`method_link_species_set_id`,`dnafrag_start`,`dnafrag_end`), KEY `node_id` (`node_id`) ) ENGINE=MyISAM AUTO_INCREMENT=6770002296671 DEFAULT CHARSET=latin1 MAX_ROWS=1000000000 AVG_ROW_LENGTH=60; CREATE TABLE `genomic_align_block` ( `genomic_align_block_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0, `score` double DEFAULT NULL, `perc_id` tinyint(3) unsigned DEFAULT NULL, `length` int(10) NOT NULL, `group_id` bigint(20) unsigned DEFAULT NULL, `level_id` tinyint(2) unsigned NOT NULL DEFAULT 0, PRIMARY KEY (`genomic_align_block_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`) ) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1; CREATE TABLE `genomic_align_tree` ( `node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `parent_id` bigint(20) unsigned DEFAULT NULL, `root_id` bigint(20) unsigned NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT 0, `left_node_id` bigint(10) DEFAULT NULL, `right_node_id` bigint(10) DEFAULT NULL, `distance_to_parent` double NOT NULL DEFAULT 1, PRIMARY KEY (`node_id`), KEY `parent_id` (`parent_id`), KEY `left_index` (`root_id`,`left_index`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `hmm_annot` ( `seq_member_id` int(10) unsigned NOT NULL, `model_id` varchar(40) DEFAULT NULL, `evalue` float DEFAULT NULL, PRIMARY KEY (`seq_member_id`), KEY `model_id` (`model_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `hmm_curated_annot` ( `seq_member_stable_id` varchar(40) NOT NULL, `model_id` varchar(40) DEFAULT NULL, `library_version` varchar(40) NOT NULL, `annot_date` timestamp NOT NULL DEFAULT current_timestamp(), `reason` mediumtext DEFAULT NULL, PRIMARY KEY (`seq_member_stable_id`), KEY `model_id` (`model_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `hmm_profile` ( `model_id` varchar(40) NOT NULL, `name` varchar(40) DEFAULT NULL, `type` varchar(40) NOT NULL, `compressed_profile` mediumblob DEFAULT NULL, `consensus` mediumtext DEFAULT NULL, PRIMARY KEY (`model_id`,`type`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `homology` ( `homology_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `method_link_species_set_id` int(10) unsigned NOT NULL, `description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') NOT NULL, `is_tree_compliant` tinyint(1) NOT NULL DEFAULT 0, `dn` float(10,5) DEFAULT NULL, `ds` float(10,5) DEFAULT NULL, `n` float(10,1) DEFAULT NULL, `s` float(10,1) DEFAULT NULL, `lnl` float(10,3) DEFAULT NULL, `species_tree_node_id` int(10) unsigned DEFAULT NULL, `gene_tree_node_id` int(10) unsigned DEFAULT NULL, `gene_tree_root_id` int(10) unsigned DEFAULT NULL, `goc_score` tinyint(3) unsigned DEFAULT NULL, `wga_coverage` decimal(5,2) DEFAULT NULL, `is_high_confidence` tinyint(1) DEFAULT NULL, PRIMARY KEY (`homology_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`), KEY `species_tree_node_id` (`species_tree_node_id`), KEY `gene_tree_node_id` (`gene_tree_node_id`), KEY `gene_tree_root_id` (`gene_tree_root_id`) ) ENGINE=MyISAM AUTO_INCREMENT=100990070 DEFAULT CHARSET=latin1; CREATE TABLE `homology_member` ( `homology_id` int(10) unsigned NOT NULL, `gene_member_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned DEFAULT NULL, `cigar_line` mediumtext DEFAULT NULL, `perc_cov` float unsigned DEFAULT 0, `perc_id` float unsigned DEFAULT 0, `perc_pos` float unsigned DEFAULT 0, PRIMARY KEY (`homology_id`,`gene_member_id`), KEY `gene_member_id` (`gene_member_id`), KEY `seq_member_id` (`seq_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=300000000; CREATE TABLE `mapping_session` ( `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `type` enum('family','tree','hmm') DEFAULT NULL, `when_mapped` timestamp NOT NULL DEFAULT current_timestamp(), `rel_from` int(10) unsigned DEFAULT NULL, `rel_to` int(10) unsigned DEFAULT NULL, `prefix` char(4) NOT NULL, PRIMARY KEY (`mapping_session_id`), UNIQUE KEY `type` (`type`,`rel_from`,`rel_to`,`prefix`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `member_xref` ( `gene_member_id` int(10) unsigned NOT NULL, `dbprimary_acc` varchar(10) NOT NULL, `external_db_id` int(10) unsigned NOT NULL, PRIMARY KEY (`gene_member_id`,`dbprimary_acc`,`external_db_id`), KEY `external_db_id` (`external_db_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `meta` ( `meta_id` int(11) NOT NULL AUTO_INCREMENT, `species_id` int(10) unsigned DEFAULT 1, `meta_key` varchar(40) NOT NULL, `meta_value` text NOT NULL, PRIMARY KEY (`meta_id`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)), KEY `species_value_idx` (`species_id`,`meta_value`(255)) ) ENGINE=MyISAM AUTO_INCREMENT=69 DEFAULT CHARSET=latin1; CREATE TABLE `method_link` ( `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `type` varchar(50) NOT NULL DEFAULT '', `class` varchar(50) NOT NULL DEFAULT '', `display_name` varchar(255) NOT NULL DEFAULT '', PRIMARY KEY (`method_link_id`), UNIQUE KEY `type` (`type`) ) ENGINE=MyISAM AUTO_INCREMENT=403 DEFAULT CHARSET=latin1; CREATE TABLE `method_link_species_set` ( `method_link_species_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `method_link_id` int(10) unsigned NOT NULL, `species_set_id` int(10) unsigned NOT NULL, `name` varchar(255) NOT NULL DEFAULT '', `source` varchar(255) NOT NULL DEFAULT 'ensembl', `url` varchar(255) NOT NULL DEFAULT '', `first_release` smallint(6) DEFAULT NULL, `last_release` smallint(6) DEFAULT NULL, PRIMARY KEY (`method_link_species_set_id`), UNIQUE KEY `method_link_id` (`method_link_id`,`species_set_id`), KEY `species_set_id` (`species_set_id`) ) ENGINE=MyISAM AUTO_INCREMENT=100070 DEFAULT CHARSET=latin1; CREATE TABLE `method_link_species_set_attr` ( `method_link_species_set_id` int(10) unsigned NOT NULL, `n_goc_null` int(11) DEFAULT NULL, `n_goc_0` int(11) DEFAULT NULL, `n_goc_25` int(11) DEFAULT NULL, `n_goc_50` int(11) DEFAULT NULL, `n_goc_75` int(11) DEFAULT NULL, `n_goc_100` int(11) DEFAULT NULL, `perc_orth_above_goc_thresh` float DEFAULT NULL, `goc_quality_threshold` int(11) DEFAULT NULL, `wga_quality_threshold` int(11) DEFAULT NULL, `perc_orth_above_wga_thresh` float DEFAULT NULL, `threshold_on_ds` int(11) DEFAULT NULL, PRIMARY KEY (`method_link_species_set_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `method_link_species_set_tag` ( `method_link_species_set_id` int(10) unsigned NOT NULL, `tag` varchar(50) NOT NULL, `value` mediumtext NOT NULL, PRIMARY KEY (`method_link_species_set_id`,`tag`), KEY `tag` (`tag`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `ncbi_taxa_name` ( `taxon_id` int(10) unsigned NOT NULL, `name` varchar(255) NOT NULL, `name_class` varchar(50) NOT NULL, KEY `taxon_id` (`taxon_id`), KEY `name` (`name`), KEY `name_class` (`name_class`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `ncbi_taxa_node` ( `taxon_id` int(10) unsigned NOT NULL, `parent_id` int(10) unsigned NOT NULL, `rank` char(32) NOT NULL DEFAULT '', `genbank_hidden_flag` tinyint(1) NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT 0, `root_id` int(10) NOT NULL DEFAULT 1, PRIMARY KEY (`taxon_id`), KEY `parent_id` (`parent_id`), KEY `rank` (`rank`), KEY `left_index` (`left_index`), KEY `right_index` (`right_index`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `other_member_sequence` ( `seq_member_id` int(10) unsigned NOT NULL, `seq_type` varchar(40) NOT NULL, `length` int(10) NOT NULL, `sequence` mediumtext NOT NULL, PRIMARY KEY (`seq_member_id`,`seq_type`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=10000000 AVG_ROW_LENGTH=60000; CREATE TABLE `peptide_align_feature` ( `peptide_align_feature_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `qmember_id` int(10) unsigned NOT NULL, `hmember_id` int(10) unsigned NOT NULL, `qgenome_db_id` int(10) unsigned DEFAULT NULL, `hgenome_db_id` int(10) unsigned DEFAULT NULL, `qstart` int(10) NOT NULL DEFAULT 0, `qend` int(10) NOT NULL DEFAULT 0, `hstart` int(11) NOT NULL DEFAULT 0, `hend` int(11) NOT NULL DEFAULT 0, `score` double(16,4) NOT NULL DEFAULT 0.0000, `evalue` double NOT NULL, `align_length` int(10) NOT NULL, `identical_matches` int(10) NOT NULL, `perc_ident` int(10) NOT NULL, `positive_matches` int(10) NOT NULL, `perc_pos` int(10) NOT NULL, `hit_rank` int(10) NOT NULL, `cigar_line` mediumtext DEFAULT NULL, PRIMARY KEY (`peptide_align_feature_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133; CREATE TABLE `seq_member` ( `seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `stable_id` varchar(128) NOT NULL, `version` int(10) DEFAULT 0, `source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL, `taxon_id` int(10) unsigned NOT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL, `sequence_id` int(10) unsigned DEFAULT NULL, `gene_member_id` int(10) unsigned DEFAULT NULL, `has_transcript_edits` tinyint(1) NOT NULL DEFAULT 0, `has_translation_edits` tinyint(1) NOT NULL DEFAULT 0, `description` text DEFAULT NULL, `dnafrag_id` bigint(20) unsigned DEFAULT NULL, `dnafrag_start` int(10) DEFAULT NULL, `dnafrag_end` int(10) DEFAULT NULL, `dnafrag_strand` tinyint(4) DEFAULT NULL, `display_label` varchar(128) DEFAULT NULL, PRIMARY KEY (`seq_member_id`), UNIQUE KEY `stable_id` (`stable_id`), KEY `taxon_id` (`taxon_id`), KEY `genome_db_id` (`genome_db_id`), KEY `source_name` (`source_name`), KEY `sequence_id` (`sequence_id`), KEY `gene_member_id` (`gene_member_id`), KEY `dnafrag_id_start` (`dnafrag_id`,`dnafrag_start`), KEY `dnafrag_id_end` (`dnafrag_id`,`dnafrag_end`), KEY `seq_member_gene_member_id_end` (`seq_member_id`,`gene_member_id`) ) ENGINE=MyISAM AUTO_INCREMENT=100289438 DEFAULT CHARSET=latin1 MAX_ROWS=100000000; CREATE TABLE `seq_member_projection` ( `target_seq_member_id` int(10) unsigned NOT NULL, `source_seq_member_id` int(10) unsigned NOT NULL, `identity` float(5,2) NOT NULL, PRIMARY KEY (`target_seq_member_id`), KEY `source_seq_member_id` (`source_seq_member_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `seq_member_projection_stable_id` ( `target_seq_member_id` int(10) unsigned NOT NULL, `source_stable_id` varchar(128) NOT NULL, PRIMARY KEY (`target_seq_member_id`), KEY `source_stable_id` (`source_stable_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `sequence` ( `sequence_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `length` int(10) NOT NULL, `md5sum` char(32) NOT NULL, `sequence` longtext NOT NULL, PRIMARY KEY (`sequence_id`), KEY `md5sum` (`md5sum`) ) ENGINE=MyISAM AUTO_INCREMENT=100259313 DEFAULT CHARSET=latin1 MAX_ROWS=10000000 AVG_ROW_LENGTH=19000; CREATE TABLE `species_set` ( `species_set_id` int(10) unsigned NOT NULL, `genome_db_id` int(10) unsigned NOT NULL, PRIMARY KEY (`species_set_id`,`genome_db_id`), KEY `genome_db_id` (`genome_db_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `species_set_header` ( `species_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(255) NOT NULL DEFAULT '', `size` int(10) unsigned NOT NULL, `first_release` smallint(6) DEFAULT NULL, `last_release` smallint(6) DEFAULT NULL, PRIMARY KEY (`species_set_id`) ) ENGINE=MyISAM AUTO_INCREMENT=36174 DEFAULT CHARSET=latin1; CREATE TABLE `species_set_tag` ( `species_set_id` int(10) unsigned NOT NULL, `tag` varchar(50) NOT NULL, `value` mediumtext NOT NULL, PRIMARY KEY (`species_set_id`,`tag`), KEY `tag` (`tag`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `species_tree_node` ( `node_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `parent_id` int(10) unsigned DEFAULT NULL, `root_id` int(10) unsigned DEFAULT NULL, `left_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT 0, `distance_to_parent` double DEFAULT 1, `taxon_id` int(10) unsigned DEFAULT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL, `node_name` varchar(255) DEFAULT NULL, PRIMARY KEY (`node_id`), KEY `taxon_id` (`taxon_id`), KEY `genome_db_id` (`genome_db_id`), KEY `parent_id` (`parent_id`), KEY `root_id` (`root_id`,`left_index`) ) ENGINE=MyISAM AUTO_INCREMENT=40102221 DEFAULT CHARSET=latin1; CREATE TABLE `species_tree_node_attr` ( `node_id` int(10) unsigned NOT NULL, `nb_long_genes` int(11) DEFAULT NULL, `nb_short_genes` int(11) DEFAULT NULL, `avg_dupscore` float DEFAULT NULL, `avg_dupscore_nondub` float DEFAULT NULL, `nb_dubious_nodes` int(11) DEFAULT NULL, `nb_dup_nodes` int(11) DEFAULT NULL, `nb_genes` int(11) DEFAULT NULL, `nb_genes_in_tree` int(11) DEFAULT NULL, `nb_genes_in_tree_multi_species` int(11) DEFAULT NULL, `nb_genes_in_tree_single_species` int(11) DEFAULT NULL, `nb_nodes` int(11) DEFAULT NULL, `nb_orphan_genes` int(11) DEFAULT NULL, `nb_seq` int(11) DEFAULT NULL, `nb_spec_nodes` int(11) DEFAULT NULL, `nb_gene_splits` int(11) DEFAULT NULL, `nb_split_genes` int(11) DEFAULT NULL, `root_avg_gene` float DEFAULT NULL, `root_avg_gene_per_spec` float DEFAULT NULL, `root_avg_spec` float DEFAULT NULL, `root_max_gene` int(11) DEFAULT NULL, `root_max_spec` int(11) DEFAULT NULL, `root_min_gene` int(11) DEFAULT NULL, `root_min_spec` int(11) DEFAULT NULL, `root_nb_genes` int(11) DEFAULT NULL, `root_nb_trees` int(11) DEFAULT NULL, PRIMARY KEY (`node_id`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `species_tree_node_tag` ( `node_id` int(10) unsigned NOT NULL, `tag` varchar(50) NOT NULL, `value` mediumtext NOT NULL, KEY `node_id_tag` (`node_id`,`tag`), KEY `tag` (`tag`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `species_tree_root` ( `root_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL, `label` varchar(256) NOT NULL DEFAULT 'default', PRIMARY KEY (`root_id`), UNIQUE KEY `method_link_species_set_id` (`method_link_species_set_id`,`label`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `stable_id_history` ( `mapping_session_id` int(10) unsigned NOT NULL, `stable_id_from` varchar(40) NOT NULL DEFAULT '', `version_from` int(10) unsigned DEFAULT NULL, `stable_id_to` varchar(40) NOT NULL DEFAULT '', `version_to` int(10) unsigned DEFAULT NULL, `contribution` float DEFAULT NULL, PRIMARY KEY (`mapping_session_id`,`stable_id_from`,`stable_id_to`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1; CREATE TABLE `synteny_region` ( `synteny_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `method_link_species_set_id` int(10) unsigned NOT NULL, PRIMARY KEY (`synteny_region_id`), KEY `method_link_species_set_id` (`method_link_species_set_id`) ) ENGINE=MyISAM AUTO_INCREMENT=51494 DEFAULT CHARSET=latin1;