An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.
We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button.
Improved taxonomic assignment
Now RAPT verifies the scientific name you provide with the reads, and corrects it as needed with the Average Nucleotide Identity (ANI) tool, which compares your genome to type strain assemblies in GenBank to place it in the taxonomic tree. So, even if you only have a rough idea of the species you have sequenced, input datasets tailored to your genome will be used for the annotation and you will get the best possible gene set from RAPT. Continue reading “New in RAPT: Better taxonomic assignment and GO annotation”→
The annotation of human assemblies GRCh38.p14 and T2T-CHM13v2.0
We are happy to announce the first de novo annotation of human T2T-CHM13v2.0, the gap-less assembly generated by the T2T Consortium, and the full re-annotation of the human reference assembly, GRCh38.p14. We hope the results will serve both the needs of those eager to explore newly sequenced regions of the genome, including telomeres and centromeres, and those interested in refreshing their interpretation of the human reference, in light of recently curated transcripts and new transcriptomic and other data incorporated in the annotation. Continue reading “Announcing Human Annotation Release 110”→
RefSeq release 212 is now available online, from the FTP site and through NCBI’s Entrez
programming utilities, E-utilities.
This full release incorporates genomic, transcript, and protein data available as of May 2, 2022, and contains 314,915,153 records, including 229,417,182 proteins, 44,805,833 RNAs, and sequences from 119,373 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.
RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. Over the years we have received many requests to add GO terms to the annotations we provide. We heard you!
We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to genomes and proteins we annotate with the Prokaryotic Genome Annotation Pipeline (PGAP). Because of the hierarchical nature of the Gene Ontologies, these annotations will help the comparison of gene content across genomes at variable levels of specificity and eventually allow GO term enrichment analysis. GO terms are now associated with coding sequence (CDS) features on newly-submitted genomes (See Figure 1). They will progressively appear on genomes that are already in RefSeq as these get reannotated (about once a year). We expect all RefSeq genomes to have some GO terms by the spring of 2023.
NCBI Gene now has descriptive information about genes from the Alliance of Genome Resources for organisms including Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, and Saccharomyces cerevisiae.
Figure 1. The gene summary section of the Drosophila melanogaster slmb Gene Full Report showing the link to the corresponding record at the Alliance of Genome Resources.
The Summary section of the Gene Full Report page has Links to gene pages at the Alliance of Genome Resources (Figure 1). These are also in the right-hand sidebar of the Links to other resources section. In the case of genes that don’t have a RefSeq summary, we use the textual gene descriptions from the Alliance of Genome resources.
The Drosphilaslmb gene record shows the enhancements provided by the Alliance of Genome Resources. The gene_info.gz files on the Gene FTP site also include AllianceGenome references in the dbXrefs column.
We are happy to announce an updated bacterial and archaeal representative genomes collection. The current collection contains a total of 15,507 assemblies selected from 236,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by five percent since August 2021. A total of 685 species are represented for the first time. In addition, 370 species are represented by a better assembly, and 84 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.