   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned DEFAULT NULL,
+  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
   KEY `operon_idx` (`operon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon_transcript_gene` (
   `operon_transcript_id` int(10) unsigned DEFAULT NULL,
   `gene_id` int(10) unsigned DEFAULT NULL,
   KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `peptide_archive` (
-  `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
   `md5_checksum` varchar(32) DEFAULT NULL,
   `peptide_seq` mediumtext NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_exon` (
   `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `prediction_transcript_id` int(10) unsigned NOT NULL,
-  `exon_rank` smallint(5) unsigned NOT NULL,
-  `seq_region_id` int(10) unsigned NOT NULL,
-  `seq_region_start` int(10) unsigned NOT NULL,
-  `seq_region_end` int(10) unsigned NOT NULL,
-  `seq_region_strand` tinyint(4) NOT NULL,
-  `start_phase` tinyint(4) NOT NULL,
+  `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+  `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+  `start_phase` tinyint(4) NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `p_value` double DEFAULT NULL,
   PRIMARY KEY (`prediction_exon_id`),
-  KEY `transcript_idx` (`prediction_transcript_id`),
-  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM ;
+  KEY `prediction_transcript_id` (`prediction_transcript_id`),
+  KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_transcript` (
   `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `seq_region_id` int(10) unsigned NOT NULL,
-  `seq_region_start` int(10) unsigned NOT NULL,
-  `seq_region_end` int(10) unsigned NOT NULL,
-  `seq_region_strand` tinyint(4) NOT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+  `analysis_id` int(11) DEFAULT NULL,
   `display_label` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
-  KEY `analysis_idx` (`analysis_id`),
-  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM ;
+  KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+  KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `protein_align_feature` (
   `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `seq_region_id` int(10) unsigned NOT NULL,
-  `seq_region_start` int(10) unsigned NOT NULL,
-  `seq_region_end` int(10) unsigned NOT NULL,
+  `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+  `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
-  `hit_start` int(10) NOT NULL,
-  `hit_end` int(10) NOT NULL,
-  `hit_name` varchar(40) NOT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `hit_start` int(10) NOT NULL DEFAULT '0',
+  `hit_end` int(10) NOT NULL DEFAULT '0',
+  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
   `perc_ident` float DEFAULT NULL,
-  `cigar_line` text,
-  `external_db_id` int(10) unsigned DEFAULT NULL,
+  `cigar_line` text COLLATE latin1_bin,
+  `external_db_id` smallint(5) unsigned DEFAULT NULL,
   `hcoverage` double DEFAULT NULL,
   PRIMARY KEY (`protein_align_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),

  PRIMARY KEY (`intron_supporting_evidence_id`),
  UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM ;

CREATE TABLE `karyotype` (
  `karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `seq_region_id` int(10) unsigned NOT NULL,
  `seq_region_start` int(10) unsigned NOT NULL,
  `seq_region_end` int(10) unsigned NOT NULL,
  `band` varchar(40) DEFAULT NULL,
  `stain` varchar(40) DEFAULT NULL,
  PRIMARY KEY (`karyotype_id`),
  KEY `region_band_idx` (`seq_region_id`,`band`)
) ENGINE=MyISAM ;

CREATE TABLE `map` (
  `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `map_name` varchar(30) NOT NULL,
  PRIMARY KEY (`map_id`)
) ENGINE=MyISAM ;

CREATE TABLE `mapping_session` (
  `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `old_db_name` varchar(80) NOT NULL DEFAULT '',
  `new_db_name` varchar(80) NOT NULL DEFAULT '',
  `old_release` varchar(5) NOT NULL DEFAULT '',

  UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
  KEY `df_name_idx` (`name`),
  KEY `df_analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

CREATE TABLE `density_feature` (
  `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
  `density_type_id` int(11) NOT NULL DEFAULT '0',
  `seq_region_id` int(11) NOT NULL DEFAULT '0',
  `seq_region_start` int(11) NOT NULL DEFAULT '0',
  `seq_region_end` int(11) NOT NULL DEFAULT '0',
  `density_value` float NOT NULL DEFAULT '0',
  PRIMARY KEY (`density_feature_id`),
  KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
  KEY `seq_region_id_idx` (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

CREATE TABLE `density_type` (
  `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
  `analysis_id` int(11) NOT NULL DEFAULT '0',
  `block_size` int(11) NOT NULL DEFAULT '0',
  `region_features` int(11) NOT NULL DEFAULT '0',
  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
  PRIMARY KEY (`density_type_id`),
  UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

CREATE TABLE `dependent_xref` (
  `object_xref_id` int(10) unsigned NOT NULL,
