REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
نویسندگان
چکیده
منابع مشابه
REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes ...
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 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...
متن کاملMIPS bacterial genomes functional annotation benchmark dataset
MOTIVATION Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. RE...
متن کاملAn Agent-Based System for Re-annotation of Genomes
Genome annotation projects can produce incorrect results if they are based on obsolete data or inappropriate models. We have developed an automatic re-annotation system that uses agents to perform repetitive tasks and reports the results to the user. These tasks involve BLAST searches on biological databases (GenBank) and the use of detection tools (Genemark and Glimmer) to identify new open re...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2017
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkx758