Category Archives: Basic Local Alignment Search Tool (BLAST)
Cleaner BLAST Databases for More Accurate Results
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 … Continue reading Cleaner BLAST Databases for More Accurate Results
BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024
Easily generate BLAST FASTA files yourself! In April 2024, the FASTA (sequence text) files of the sequences in the Basic Alignment Search Tool (BLAST) databases will no longer be available on the FTP site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes … Continue reading BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024
Posted by in Basic Local Alignment Search Tool (BLAST), FASTA, NCBI Taxonomy, What's New
Updated Bacterial and Archaeal Reference Genome Collection is Available!
Download the updated bacterial and archaeal reference genome collection! This collection of 18,943 genomes 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 … Continue reading Updated Bacterial and Archaeal Reference Genome Collection is Available!
Using NCBI Data and Tools for Your Research Project
Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project. How and why do you use our resources? Check out the example below: Your professor has assigned you a research project looking at … Continue reading Using NCBI Data and Tools for Your Research Project
Faster and Focused Searches with BLAST+ 2.15.0
New version now available Do you use NCBI’s standalone BLAST tool (BLAST+)? The latest version of BLAST+ is now available and includes two exciting new features! You can now run searches faster and focus your searches by organism more easily. What’s new? Run searches faster BLAST+ now runs 2-10x faster for small databases and … Continue reading Faster and Focused Searches with BLAST+ 2.15.0
Posted by in Basic Local Alignment Search Tool (BLAST), BLAST, What's New
Comparing Yeast Species Used in Beer Brewing and Bread Making
Using the NIH Comparative Genomics Resource (CGR) to gain knowledge about less-researched organisms The scientific community relies heavily on model organism research to gain knowledge and make discoveries. However, focusing solely on these species misses valuable variation. Comparative genomics allows us to use knowledge from a model species, such as Saccharomyces cerevisiae, to understand traits in … Continue reading Comparing Yeast Species Used in Beer Brewing and Bread Making
BLAST ClusteredNR Database is Now Available for Download!
Now available! You can download the ClusteredNR protein database, previously only available on the BLAST web application. As recently introduced, our ClusteredNR database allows you to get quicker BLAST results and access to information about the distribution of your hits across a wider range of organisms and evolutionary distances. The package includes the ClusteredNR BLAST … Continue reading BLAST ClusteredNR Database is Now Available for Download!
Now Available! Updated Bacterial and Archaeal Reference Genomes Collection
An updated bacterial and archaeal reference genome collection is available! This collection of 18,343 genomes was built by selecting exactly one genome assembly for each species among the 312,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference. The criteria for selecting the reference assembly for a given species include assembly contiguity … Continue reading Now Available! Updated Bacterial and Archaeal Reference Genomes Collection
Which animals can catch and transmit human viral infections?
Using the NIH Comparative Genomics Resource (CGR) to understand susceptibility to SARS-CoV-2 and other infections Are you conducting research on animal-mediated transmission of human viral infections, such as COVID-19? The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help with comparative genomics … Continue reading Which animals can catch and transmit human viral infections?
New & Improved NCBI Datasets Genome and Assembly Pages
Legacy pages now redirect Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data. The following pages have … Continue reading New & Improved NCBI Datasets Genome and Assembly Pages