Some of these methods include sequence similarity, phylogenomic o

Some of these methods include sequence similarity, phylogenomic or genomic context, metabolic reconstruction to determine pathway holes, comparative genomics, and in many cases a combination of all of the above (reviewed in [20]). A number of tools have been developed to predict annotations based on curated and experimental data. Curated model organism databases or datasets for specific molecules such as transfer RNAs, ribosomal RNAs, or other non-coding RNAs have been developed along with tools to predict their presence in a novel sequence [21-24]. Several large-scale curated databases have been created at large centers, such as at EBI and NCBI. NCBI initiated the Reference Sequence database to create a curated non-redundant set of sequences derived from original submissions to INSDC [25]. The sequences include genomic DNA, transcripts, and proteins and the annotations may consist of submitter-derived, curated, or computational predictions. One major resource for improving functional annotation is the NCBI Protein Clusters database that consists of cliques of related proteins (ProtClustDB [26]; ). A subset of clusters are curated and utilized as sources of functional annotation in the annotation pipeline as well as to incrementally update RefSeq records (see below). RefSeq records are also updated from model organism databases such as those for E. coli K-12 or Flybase. The UniProt Knowledgebase (UniProtKB) provided by the UniProt consortium is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources [27]. The Genome Reviews portal that was a comprehensively up-to-date set of genomes has now been incorporated at ENSEMBL genomes [28,29]. Ongoing collaboration between NCBI and EBI ensures that annotation will continue to be curated and improved in all databases. RefSeq is committed to ensuring that all current and future RefSeq prokaryotic records meet the minimal standards presented in this article. However, high throughput next generation sequencing increasingly results in a large number of non-reference sequences populating the databases with the expectation that there could be tens of thousands of genomes available for all prokaryotes. Community acceptance of a set of minimal annotation standards puts the burden on all genome submitters to provide quality annotation especially for those complete genomes that are often considered gold standard records for sequencing and annotation such as Escherichia coli K-12 MG1655. The Need for Standards Standards and guidelines facilitate the submission, retrieval, exchange, and analysis of data. Both the format and content of data can be standardized (syntactic and semantic). Syntactic standardization is easier to implement and enforce. The format and representation of genomic records has long been established and is not discussed in this article. Semantic standardization is more difficult.

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