TY - JOUR
T1 - Analysis of the phage sequence space
T2 - The benefit of structured information
AU - Lima-Mendez, Gipsi
AU - Toussaint, Ariane
AU - Leplae, Raphaël
N1 - Funding Information:
We thank M. Salas, H. Krish, and E. Haggard-Ljungquist for their help in putting together more ‘user-friendly’ annotations of their favourite genome, S. Casjens and I. Molineux, G. Chaconas, A. Landy and G. Hatfull for their contribution to the assembly of phage terms and definitions and Jeanne Gouello for her contribution to the analysis of ORFan proteins. This work was supported by the Fonds de la Recherche Scientifique Médicale (FRSM) and by ESA (European Space Agency contract ESTEC 16370/02/NL/CK), and the Université Libre de Bruxelles within a collaboration with M. Mergeay and P. de Boever at the Laboratory for Microbiology, SCK-CEN, Mol Belgium. G.L-M is a fellow from the Fonds Xenophilia, ULB.
PY - 2007/9/1
Y1 - 2007/9/1
N2 - Phages are the most abundant biological entities on Earth and are central players in the evolution of their bacterial hosts and the emergence of new pathogens. In addition, they bear an enormous potential for the development of new drugs, therapies or nanotechnologies. As a result, interest in phages is reviving. In the genomic era, our perspective on the phage sequence space remains incredibly sparse. The modular and combinatorial structure of phage genomes is largely documented. It is confirmed by new sequence information and it fuels a recurrent debate on the need to revise phage taxonomy. The absence of structured, computer readable information on phages is a major bottleneck for an extensive global analysis of phage genomes and their relationships, but such information is essential to reassess phage classification. Based on the ACLAME database, which is dedicated to the organization and analysis of prokaryotic mobile genetic elements, we discuss here how structured information on phage-encoded proteins helps global in silico analysis and allows the prediction of prophages in bacterial genome sequences, providing access to additional phage sequence information.
AB - Phages are the most abundant biological entities on Earth and are central players in the evolution of their bacterial hosts and the emergence of new pathogens. In addition, they bear an enormous potential for the development of new drugs, therapies or nanotechnologies. As a result, interest in phages is reviving. In the genomic era, our perspective on the phage sequence space remains incredibly sparse. The modular and combinatorial structure of phage genomes is largely documented. It is confirmed by new sequence information and it fuels a recurrent debate on the need to revise phage taxonomy. The absence of structured, computer readable information on phages is a major bottleneck for an extensive global analysis of phage genomes and their relationships, but such information is essential to reassess phage classification. Based on the ACLAME database, which is dedicated to the organization and analysis of prokaryotic mobile genetic elements, we discuss here how structured information on phage-encoded proteins helps global in silico analysis and allows the prediction of prophages in bacterial genome sequences, providing access to additional phage sequence information.
KW - Bacteriophages
KW - Comparative genomics
KW - Phage classification
KW - Prophage detection
UR - http://www.scopus.com/inward/record.url?scp=34547652871&partnerID=8YFLogxK
U2 - 10.1016/j.virol.2007.03.047
DO - 10.1016/j.virol.2007.03.047
M3 - Short survey
C2 - 17482656
AN - SCOPUS:34547652871
SN - 0042-6822
VL - 365
SP - 241
EP - 249
JO - Virology
JF - Virology
IS - 2
ER -