Effective August 2024, core_nt will become the default
Interested in faster nucleotide BLAST searches with more focused search results? As previously announced, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI’s BLAST is excited to introduce the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size.
Benefits of BLAST core_nt over nt
Enables faster searches
Returns similar top results for most searches
Reduces redundancy for some highly represented organisms
Allows easier download and requires less storage space for database download for standalone BLAST
Find evolutionarily related genes across insects and otherarthropods on our new Ortholog webpages
NCBI recently released a set of orthologs for approximately 2 million insect genes. You can now find and access the orthologous genes, transcripts, and proteins by searching a species and gene name in NCBI All Databases, NCBI Gene, or NCBI Datasets. As previously described, these orthologs are based on comparisons to the Drosophila melanogaster annotated genome. Using Drosophila gene nomenclature for orthologs should lead to more informative gene symbols for insects and other arthropods.Continue reading “Ortholog Groups Added for ~2 Million Insect Genes”→
Removing contaminated sequences using NCBI quality assurance tools
Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.Continue reading “Cleaner BLAST Databases for More Accurate Results”→
New & improved NCBI Datasets Taxonomy pages and command-line service
NCBI Datasets is excited to introduce new features to our Taxonomy pages making it easier for you to access, browse, and download taxonomic information about organisms at any taxonomic level.
What’s new?
Explore Taxonomy records with an updated look and feel
Access and download taxonomic metadata from the web or with our updated command-line (CLI) tools
Do you submit genome assembly data to GenBank? If so, try out NCBI’s Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. We will screen all prokaryotic and eukaryotic genome submissions to GenBank with this tool, but we encourage you to screen your data before submitting to save time. FCS offers sensitive contaminant detection to increase the quality of your genome submissions to GenBank. As part of our ongoing effort to improve your experience, we recently made several enhancements.Continue reading “Foreign Contamination Screen Tool: Now Available in Galaxy!”→
