Concordance analysis of microbial genomes

• Published in: Nucleic acids research Vol. 26; no. 19; pp. 4482 - 4486
• Main Authors: Bruccoleri, Robert E., Dougherty, Thomas J., Davison, Daniel B.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.10.1998
• Subjects: Bacteria - genetics; Databases, Factual; Genes, Bacterial; Genome, Bacterial; Sequence Analysis, DNA - methods
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/26.19.4482

The set of proteins which are conserved across families of microbes contain important targets of new anti-microbial agents. We have developed a simple and efficient computational tool which determines concordances of putative gene products that show sets of proteins conserved across one set of user specified genomes and not present in another set of user specified genomes. The thresholds and the homology scoring criterion are selectable to allow the user to decide the stringency of the homologies. The system uses a relational database to store protein coding regions from different genomes, and to store the results of a complete comparison of all sequences against all sequences using the FASTA program. Using Web technology, the display of all the related proteins for a given sequence and calculation of multiple sequence alignments (using CLUSTALW) can be performed with the click of a button. The current database holds 97 365 sequences from 19 complete or partial genomes and 8 798 905 FASTA comparison results. A example concordance is presented which demonstrates that the target of the quinolone antibiotics could have been identified using this tool.