Category Archives: downloading data
June 30 Webinar: Using NCBI Datasets to download sequence and annotation for genomes and genes
Join us on June 30, 2021 at 12PM eastern time to learn how to use the new NCBI Datasets resource to find and download gene, genome and SARS-CoV-2 sequence and annotation. You will learn how to access these datasets through either the web interface or the new command-line tools that allow you to incorporate these data … Continue reading June 30 Webinar: Using NCBI Datasets to download sequence and annotation for genomes and genes
Posted by in Datasets, downloading data, SARS-CoV-2, webinars, What's New
New NCBI Datasets home and documentation pages provide easier access
NCBI Datasets, the new set of services for downloading genome assembly and annotation data (previous Datasets posts), has redesigned and reorganized web pages to make it easier to find and access the services and documentation you need. NCBI Datasets has a fresh new homepage (Figure 1) highlighting the types of data available through our tools. Available … Continue reading New NCBI Datasets home and documentation pages provide easier access
Posted by in Datasets, downloading data, Gene, genome annotation, genome assemblies, SARS-CoV-2, Viruses, What's New
The Datasets command-line tool now provides ortholog data
You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish. (See our recent post for more information on the orthologs for fish and insects.) You … Continue reading The Datasets command-line tool now provides ortholog data
Posted by in Datasets, downloading data, Gene, homologs, RefSeq, What's New
The Datasets command-line tool now provides ortholog data
You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish. (See our recent post for more information on the orthologs for fish and insects.) You … Continue reading The Datasets command-line tool now provides ortholog data
Posted by in Datasets, downloading data, Gene, homologs, RefSeq, What's New
Programmatic access to Gene Data using Datasets command-line and API
In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool? Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins … Continue reading Programmatic access to Gene Data using Datasets command-line and API
Posted by in API, Datasets, downloading data, Gene, What's New
NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms
NCBI Datasets now offers Gene tables: customizable tables of the genes you specify, with key gene information, and the ability to easily download a dataset of genomic, transcript and protein sequences. Drag and drop a list of Gene IDs or gene symbols, and the data table shows your genes with up to 15 columns of metadata, … Continue reading NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms
Posted by in Datasets, downloading data, Gene, RefSeq, What's New
Easily download large amounts of genomic data with NCBI Datasets
Do you need to download a lot of genomic data? Maybe you need all primate reference genomes or maybe you need just a few really big genomes? Prior to the advent of NCBI Datasets, downloading such a large amount of data could be a frustrating and time consuming experience involving failed downloads and writing custom scripts. NCBI Datasets … Continue reading Easily download large amounts of genomic data with NCBI Datasets
Posted by in Datasets, downloading data, Genome, genome assemblies, What's New
The next RefSeq FTP release number will skip to 200
NCBI’s Reference Sequence (RefSeq) FTP release numbers will increment to 200 for the next release and skip over the numbers 100-199. The current, March 2020 release, is release 99. The next bi-monthly release in May 2020 will be release 200. … Continue reading
Posted by in downloading data, eukaryotic genome annotation, RefSeq, sequences, What's New
Important changes to the genomes FTP site in February
We have added the latest NCBI Eukaryotic Genome Annotation Pipeline results for the more than 580 species that we annotate to the genomes/refseq directory on the genomes FTP area. As we announced in December, we will stop publishing annotation results … Continue reading
New download files and FTP directories for genome assemblies
You can now download new file types for species recently annotated by the NCBI Eukaryotic Genome Annotation Pipeline from the Assembly web pages and from the genomes/refseq FTP area. The new files types include alignments of annotated transcripts to the … Continue reading
Posted by in assembly, downloading data, Genome, What's New