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NCBI prokaryotic genome annotation pipeline

Nucleic acids research, 2016-08, Vol.44 (14), p.6614-6624 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. ;Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. 2016 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkw569 ;PMID: 27342282

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  • Title:
    NCBI prokaryotic genome annotation pipeline
  • Author: Tatusova, Tatiana ; DiCuccio, Michael ; Badretdin, Azat ; Chetvernin, Vyacheslav ; Nawrocki, Eric P ; Zaslavsky, Leonid ; Lomsadze, Alexandre ; Pruitt, Kim D ; Borodovsky, Mark ; Ostell, James
  • Subjects: Bacteria - genetics ; Bacterial Proteins - chemistry ; Computational Biology ; Databases, Nucleic Acid ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Annotation ; Prokaryotic Cells - metabolism
  • Is Part Of: Nucleic acids research, 2016-08, Vol.44 (14), p.6614-6624
  • Description: Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 0305-1048
    EISSN: 1362-4962
    DOI: 10.1093/nar/gkw569
    PMID: 27342282
  • Source: GFMER Free Medical Journals
    MEDLINE
    PubMed Central
    Open Access: Oxford University Press Open Journals
    DOAJ Directory of Open Access Journals
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