MicrobeDB Overview
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MicrobeDB provides centralized storage and access to archaeal and bacterial genomes, including various file formats from NCBI RefSeq, with both published and unpublished genomes accepted. The information is parsed and stored in a MySQL database, accessible through traditional MySQL programs and a Perl MicrobeDB API. Key features include version control for genome data, detailed organization of genome projects and replicons, and comprehensive gene annotations.
MicrobeDB Overview
- 1. MicrobeDB Overview Morgan Langille morgan.gi.langille@gmail.com
- 2. Main Features Centralized storage and access to completed archaeal and bacterial genomes Genomes obtained from NCBI RefSeq: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi Genome/Flat files are stored in one central location Including files .gbk, .gff, .fna, .faa, etc. Unpublished genomes can be added as well Information at the genome project, chromosome, and gene level are parsed and stored in a MySQL database A Perl MicrobeDB API provides non-MySQL interface with the database.
- 3. Main MicrobeDB Tables Version Each download of genomes from NCBI is given a new version numbe Data will not change if you always use the same version number of microbedb Version date can be cited for any method publications A version can be saved by users so not automatically deleted. Genome Project Contains information about the genome project and the organism that was sequenced Each genome project contains one or more replicons Replicon Chromosome, plasmids, or contigs Each replicon contains one or more genes Gene Contains gene annotations and also the DNA and protein sequences (if protein coding gene)
- 5. Accessing MicrobeDB • Any traditional MySQL programs – phpMyAdmin: – Web-based – http://phpmyadmin.net – MySQL Workbench – Local desktop client – http://www.mysql.com/products/workbench/ • MicrobeDB Perl API – Allows interaction with database directly from within a Perl script – Requires no knowledge of SQL
- 7. phpMyAdmin
- 8. MicrobeDB API Example #Use the MicrobeDB Search library use MicrobeDB::Search; #create the search object my $search_obj= new MicorbeDB::Search(); #Create an object with certain features that we want (i.e. only pathogens) my $obj = new GenomeProject( version_id => '1', patho_status => 'pathogen' ); #This does the actual search and returns a list of all genome projects that match search parameters my @result_objs = $search_obj->object_search($obj); #Now we can iterate through each genome project foreach my $gp_obj (@result_objs) { #get the name of the genome $gp_obj->org_name() foreach my $gene_obj ($gp_obj->genes()){ if($gene_obj->gene_type() eq 'tRNA'){ #write the genes in fasta format with gid as the identifier print '>',$gene_obj->gid,”n”,$gene_obj->gene_seq(); }}}