The bioinformatics resource for oral pathogens.
Complete genomic sequences of several oral pathogens have been deciphered and multiple sources of independently annotated data are available for the same genomes. Different gene identification schemes and functional annotation methods used in these databases present a challenge for cross-referencing and the efficient use of the data. The Bioinformatics Resource for Oral Pathogens (BROP) aims to integrate bioinformatics data from multiple sources for easy comparison, analysis and data-mining through specially designed software interfaces. Currently, databases and tools provided by BROP include: (i) a graphical genome viewer (Genome Viewer) that allows side-by-side visual comparison of independently annotated datasets for the same genome; (ii) a pipeline of automatic data-mining algorithms to keep the genome annotation always up-to-date; (iii) comparative genomic tools such as Genome-wide ORF Alignment (GOAL); and (iv) the Oral Pathogen Microarray Database. BROP can also handle unfinished genomic sequences and provides secure yet flexible control over data access. The concept of providing an integrated source of genomic data, as well as the data-mining model used in BROP can be applied to other organisms. BROP can be publicly accessed at http://www.brop.org.
Chen
Tsute
T
The Forsyth Institute, 140 Fenway, Boston, MA 02115, USA. tchen@forsyth.org
Abbey
Kevin
K
Deng
Wen-jie
WJ
Cheng
Meng-chuan
MC
D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003196:Computer Graphics; D030541:Databases, Genetic; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D020407:Internet; D009055:Mouth / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D016966:Porphyromonas gingivalis / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software; D013295:Streptococcus mutans / Q000235:genetics; D014584:User-Computer Interface