Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
نویسندگان
چکیده
منابع مشابه
Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation p...
متن کاملAnnotation of bacterial genomes using improved phylogenomic profiles
MOTIVATION Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between ...
متن کاملThe automatic annotation of bacterial genomes
With the development of ultra-high-throughput technologies, the cost of sequencing bacterial genomes has been vastly reduced. As more genomes are sequenced, less time can be spent manually annotating those genomes, resulting in an increased reliance on automatic annotation pipelines. However, automatic pipelines can produce inaccurate genome annotation and their results often require manual cur...
متن کامل4. A new approach to the annotation of bacterial genomes using phylogenomic profiles
Phylogenomic profiling is a non-sequence-homology-based method designed to infer a likely functional relationship between proteins. It is based on the assumption that proteins involved in a common metabolic pathway are likely to evolve in a correlated manner. This paradigm was put to use by Pellegrini et al. [1] and first apply to Escherichia coli. According to this study, a phylogenomic profil...
متن کاملLarge-Scale Comparative Annotation of Bacterial Genomes
The MSc thesis describes the design and evaluation of a comparative annotation system for prokaryotic genomes. The proposed system makes use of a combination of comparative and abinitio gene finding techniques for accurate annotation. The three main modules described in the system are the markov-model based gene finding module, the alignment based profiler and the comparative module that combin...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2003
ISSN: 1362-4962
DOI: 10.1093/nar/gkg603