Overview of MicrobeDB
By Morgan Langille

MicrobeDB
 Centralized storage and access to completed Archaea and Bacteria
genomes
 Same as those available at:
http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
 Genome/Flat files are stored in one central location (optional)
 E.g. “/var/opt/NCBI_genomes”
 Information at the genome project, chromosome, and gene level are parsed
and stored in a MySQL database (MicrobeDB)
 including sequences and annotations
 The files and the database can be easily updated monthly

MicrobeDB
MicrobeDB MySQL
Schema
October 23, 2006 Brinkman Lab Presentation 3

MicrobeDB Overview
NCBI Download Parse
Annotation Load MicrobeDB
Perl API
MicrobeDB
(MySQL)
Access MicrobeDB
Perl API
Your Perl Script
Results
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MicrobeDB Versioning
 Version
 Each monthly download from NCBI is given a new version number
 Advantages
 Data will not change if you always use the same version number of microbedb
 Version date can be cited for any method publications
 Disadvantages
 Data is redundant in the database (e.g. multiple versions of the same gene)
 A version number (version_id) must always be used when retrieving
information otherwise multiple copies will be returned

MicrobeDB Tables
 Genomeproject
 Contains information about the genome project and the organism that was sequenced
 E.g. taxon_id, org_name, lineage, gram_stain, genome_gc, patho_status, disease, genome_size,
pathogenic_in, temp_range, habitat, shape, arrangement, endospore, motility, salinity, etc.
 Each genomeproject contains one or more replicons
 Replicon
 Chromosome or plasmids
 E.g. rep_accnum, definition, rep_type, rep_ginum, cds_num, gene_num, protein_num, genome_id, rep_size,
rna_num, rep_seq (complete nucleotide sequence)
 Each replicon contains one or more genes
 Gene
 Contains gene annotations and also the DNA and protein sequences (if protein coding gene)
 E.g. gid, pid, protein_accnum, gene_type, gene_start, gene_end, gene_length, gene_strand, gene_name,
locus_tag, gene_product, gene_seq, protein_seq
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Accessing MicrobeDB
 Direct MySQL access
 username:perlapi
 password:microbedb
OR
 Using the MicrobeDB Perl API

MicrobeDB API
 Perl Classes/Modules
 GenomeProject
 Replicon  Use these
Classes
 Gene
 Search
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MicrobeDB API Example
#Use the MicrobeDB Search library
use lib 'microbedb/MicrobeDB';
use Search;
#Create an object with certain features that we want (i.e. only chromosomes)
my $rep_obj = new Replicon( version_id => '1', rep_type => 'chromosome' );
#Create the search object.
my $search_obj = new Search();
#This does the actual search
my @result_objs = $search_obj->object_search($rep_obj);
#Now we can iterate through each replicon object that was returned
foreach my $curr_rep_obj (@result_objs) {
#get the replicon accesion
my $rep_accnum = $curr_rep_obj->rep_accnum();
#get all genes associated with this chromosome
my $genes = $curr_rep_obj->genes();
#continued next slide
October 23, 2006 Brinkman Lab Presentation 9

MicrobeDB API Example cont.
#print out all genes that are annotated as 16s RNA in FASTA format
foreach $curr_gene (@$genes){
#Only look at rRNA genes
if($curr_gene->gene_type() eq 'rRNA'){
$rna_product = $curr_gene->gene_product();
#check to see if the gene is annotated as a 16s rRNA
if(defined($rna_product) && $curr_gene->gene_product =~ /16s/i){
$gid = $curr_gene->gid();
$start = $curr_gene->gene_start();
$end = $curr_gene->gene_end();
$seq = $curr_gene->gene_seq();
#print out the gene in fasta format
print ">$rep_accnum|gi:$gid|$start - $end|$rna_productn";
print $seq . "n";
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