Tag: RefSeq
During October to January, the NCBI Eukaryotic Genome Annotation Pipeline released seventy new annotations in RefSeq!
Download the updated bacterial and archaeal reference genome collection! This collection (18,941 genomes as of Jan 18, 2024) was built by selecting the “best” genome assembly for each species among the 330,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). You can speed up your sequence searches by running them against these high-quality genomes instead of the entire nucleotide or protein database.
The criteria for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation. Continue reading “Updated Bacterial and Archaeal Reference Genome Collection is Available!”
Check out RefSeq release 222, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.
As of January 8, 2024, this full release incorporates genomic, transcript, and protein data containing:
Download release 14.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. Continue reading “Now Available: NCBI Hidden Markov Models (HMM) Release 14.0!”
Are you interested in more functional information about protein-coding genes? We’ve expanded NCBI RefSeq’s Eukaryote Genome Annotation Pipeline (EGAP) to include Gene Ontology (GO) terms computed for most protein-coding genes. We are using the latest version of InterProScan, which now includes analysis based on PANTHER reference trees, on all NCBI RefSeq eukaryotic genomes. That means having comprehensive GO data with inferred biological process, molecular function, and cellular component terms matched with high-quality RefSeq annotations across hundreds of taxa to help drive your research. The data is available on individual records in NCBI’s Gene resource, NCBI Gene FTP, or in community standard .gaf formatted files with each RefSeq genome release on our FTP site. Continue reading “Gene Ontology (GO) Terms for NCBI RefSeq Eukaryotic Genomes”
RefSeq release 221 is now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.
As of November 6, 2023, this full release incorporates genomic, transcript, and protein data containing:
Do you need to compare and combine data based on NCBI RefSeq and UniProt datasets, and aren’t sure which proteins are comparable? For many years, NCBI Gene has provided information about the relationships between RefSeq and UniProt accessions courtesy of data imported from UniProt, but the tremendous growth of both datasets has led to large gaps in the data. We have developed a new process to compare the two datasets, first looking for 100% identical proteins and then checking the remaining sequences for similar matches in related taxa. The result is mapping information now covering over 170 million RefSeq proteins across the tree of life.
You can find links to related UniProt accessions on individual NCBI Gene records. The entire dataset is available on our FTP site. Continue reading “Now Available! Compare NCBI RefSeq and UniProt Datasets”
In July, August, and September, the NCBI Eukaryotic Genome Annotation Pipeline released fifty-six new annotations in RefSeq!
Coming soon! As part of our ongoing effort to enhance your experience and modernize our services, several of our legacy virus-related web resources will be replaced by NCBI Virus – our community portal for viral sequence data. NCBI Virus is more comprehensive, modernized, and has more powerful features and analysis tools than our legacy resources.
Below is a list of the legacy virus resources that will be replaced by NCBI Virus. The list includes a description of features that will continue to be supported through NCBI Virus: Continue reading “Upcoming Changes to Virus Data Resources at NCBI”
As part of our ongoing effort to modernize and improve your experience, we are excited to introduce the new NCBI Datasets genome annotation table. You can now quickly and easily access annotated gene and protein sequences annotated by NCBI RefSeq or GenBank submitters.
Continue reading “Introducing the New NCBI Datasets Genome Annotation Table”