NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Abstract

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16,00 organisms, 2.4 × 0(6) genomic records, 13 × 10(6) proteins and 2 × 10(6) RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).

Figure 1.

NM_145204.3 is shown in the Nucleotide Graphical display format. The display was configured to show the six-frame translation track restricted to the sense strand, and to add three markers highlighting the annotated upstream in-frame stop codon, the translation initiation codon and a second in-frame AUG codon located further downstream. The observation of a stop codon upstream of, and in the same reading frame, suggests the annotated CDS is 5′ complete.