Tag: Basic Local Alignment Search Tool (BLAST)

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 been updated:

The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST. 
The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.

During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024.  Continue reading “New & Improved NCBI Datasets Genome and Assembly Pages “ →

Revolutionize your research with the NIH Comparative Genomics Resource (CGR)

Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.  

Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)” →

Navigating Between BLAST and iCn3D

Explore protein structures and sequences quickly and easily

Have you ever come across an unfamiliar protein in your BLAST results? With the newly added ‘AlphaFold Structure’ link (Figure 1), you can now explore its structure as predicted by AlphaFold in iCn3D. The iCn3D Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool with interactive displays of 3D structure, 2D topology, 1D sequence and annotation.

Features & Benefits

Upload AlphaFold structures to iCn3D directly
Use the structure search feature to find structures of interest
Understand important features of the structures, such as disease-associated variations (ClinVar), genetic variations (dbSNP), or chemical modifications (PTM)
Identify similarities and differences between AlphaFold predictions and experimentally determined structure
Gain insights into the structural characteristics and properties of the molecules
Use iCn3D in different platforms (Jupyter Notebook, Virtual Reality, and Augmented Reality)
Easily integrate iCn3D using scripted workflows (node.js, python) to analyze large sets of structures

Continue reading “Navigating Between BLAST and iCn3D” →

Now Available! Faster BLAST Searches with New Nucleotide Databases

NEW in BLAST! We made smaller nucleotide databases to help you find the sequences you need faster and easier. You can now find these databases on the main nucleotide BLAST search page (Figure 1) and even download them (Databases: nt_euk, nt_prok, nt_viruses, nt_others). They are separated by organism type, such as eukaryotes, prokaryotes, viruses, and others (including synthetic sequences).

Figure 1. The database selection section of the main nucleotide BLAST page with the ‘Experimental databases’ radio button selected. You can choose one or more of the organism database subsets for your search. Continue reading “Now Available! Faster BLAST Searches with New Nucleotide Databases” →

New Release! Updated Bacterial and Archaeal Reference Genomes Collection Now Available

As previously announced, we are continuously curating a better Prokaryotic Reference Genomes Collection. An updated bacterial and archaeal reference genome collection is now available! This collection of 17,623 genomes was built by selecting exactly one genome assembly for each species among the 283,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

What’s new?

480 species were added to this collection
178 species are represented by a better assembly
17 species were removed due to changes in NCBI Taxonomy or uncertainty in their species assignment

Continue reading “New Release! Updated Bacterial and Archaeal Reference Genomes Collection Now Available” →

Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue

The 2023 Nucleic Acids Research Database Issue features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below. Continue reading “Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue” →

Now Available! Add your favorite organism(s) to your BLAST ClusteredNR searches

Do you currently add an organism name(s) to focus your searches when using the BLAST standard nr database? You can now focus your searches by organism with the BLAST ClusteredNR database and get faster results with a better overview of protein homologs in a wider range of organisms. Your searches will be restricted to protein clusters that contain one or more sequences from the organism(s) you add.

ClusteredNR results

A search of the ClusteredNR database (results) using human myoglobin (NP_005359.1) as a query and limited to Cetacea (whales & dolphins) returns clusters containing all the whale myoglobin matches present in a search of standard nr, as well as matches to clusters containing cytoglobin (Figure 1 A). These significant cytoglobin matches are not shown in the standard nr results with the Cetacea limit, which are dominated by matches to proteins from a single species, Physeter catodon (sperm whale) (Figure 1 B). Continue reading “Now Available! Add your favorite organism(s) to your BLAST ClusteredNR searches” →

Updated bacterial and archaeal reference genomes collection now available!

An updated bacterial and archaeal reference genome collection is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

A total of 497 species are included in this collection for the first time. In addition, comparing to the October 2022 set, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the documentation for details.

We have updated the nucleotide BLAST RefSeq reference genomes database (fourth in the menu) as well as the database on the Microbial Nucleotide BLAST page to reflect these changes. You can also run BLAST searches against the proteins annotated on these reference genomes (RefSeq Select proteins database, second in the menu).

NIH Comparative Genomics Resource project

The potential impact of emerging model organisms on human health

Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health. Continue reading “NIH Comparative Genomics Resource project” →

Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches

ClusteredNR, the new protein database that provides results with a better overview of protein homologs in a wider range of organisms, is now available for blastx (translated nucleotide query) and PSI-BLAST (Position Specific Iterative BLAST) searches (Figure 1). Simply select ClusteredNR in the database section of the BLAST form. You can even search standard nr at the same time to compare results.

Figure 1. Composite image from the BLAST search forms. The ClusteredNR database is available now for blastx and PSI-BLAST searches in addition to blastp. For all types of searches, you can choose to search both ClusteredNR and standard nr at the same time so you can compare results

ClusteredNR is especially useful with blastx for finding more distant homologs when searching with queries from over-represented groups. For PSI-BLAST, the greater taxonomic scope of ClusteredNR database allows you to work more effectively with the default number target sequences in the first round. The two searches described below highlight these advantages of ClusteredNR.

Continue reading “Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches” →