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Item does not contain fulltext, Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.

01 januari 2012, Item does not contain fulltext, OBJECTIVES: To identify appropriate screening conditions, stratified according to age and vulnerability, to prevent functional decline in older people. DESIGN: A RAND/University of California at Los Angeles appropriateness method. SETTING: The Netherlands. PARTICIPANTS: A multidisciplinary panel of 11 experts. MEASUREMENTS: The panelists assessed the appropriateness of screening for 29 conditions mentioned in guidelines from four countries, stratified according to age (60-74, 75-84, >/=85) and health status (general, vital, and vulnerable) and received a literature overview for each condition, including the guidelines and up-to-date literature. After an individual rating round, panelists discussed disagreements and performed a second individual rating. The median of the second ratings defined the appropriateness of screening. RESULTS: The panel rated screening to be appropriate in three of the 29 conditions, indicating that screening was expected to prevent functional decline. Screening for insufficient physical activity was considered appropriate for all three age and health groups. Screening for cardiovascular risk factors and smoking was considered appropriate for the general and vital population aged 60 to 74. Of the 261 ratings, 63 (24%) were classified as uncertain, of which 42 (67%) concerned the vulnerable population. The panelists considered conditions inappropriate mainly because of lack of an adequate screening tool or lack of evidence of effective interventions for positive screened persons. CONCLUSION: The expert panel considered screening older people to prevent functional decline appropriate for insufficient physical activity and smoking and cardiovascular risk in specific groups. For other conditions, sufficient evidence does not support screening. Based on their experience, panelists expected benefit from developing tests and interventions, especially for vulnerable older people.