The latest improvement in the NCBI search experience is designed to help you quickly find microbial proteins. Now when you search for a prokaryotic protein name such as recombinase RecA in NCBI’s sequence databases or in the All databases search, a high-quality representative protein sequence is highlighted in a panel at the top of the results page (Figure 1).
The result panel also allows you to quickly link to related resources such as NCBI’s new pages for protein family models, Identical Protein Groups, and SPARCLE, NCBI’s protein domain architecture resource. We also provide as-you-type suggestions so you don’t have to type out some of the long names.
Figure 1. The result for a search with recombinase RecA. The panel provides access to analysis tools, downloads, and relevant links to the protein family, the RefSeq protein, the identical protein group, and citations in PubMed.
Try these protein name searches, or your own, and use the as-you-type suggestions to assist your searches.
Please let us know how you like these results!
As part of our ongoing effort to improve your search experience, we’ve made it easier for you to find the sequence of your favorite organelle genome plus all the information and data associated with it. To find organelle genomes, search for an organism name combined with an organelle description, for example human mitochondrion, tomato chloroplast or Toxoplasma gondii RH apicoplast.
A new results panel will appear with links to the organelle genome sequence, annotated genes, and related phylogenetic and population studies. The panel appears with these searches in an All Databases search or within any of NCBI’s sequence databases including Gene, Nucleotide, Protein, Genome, Assembly. For the human mitochondrial genome, a graphical schematic of the genome allows you to navigate to individual mitochondrial encoded genes (Figure 1).
Figure 1. The organelle genome results for a search with human mitochondrion. The panel provides access to analysis tools, downloads, and other relevant results. Clicking any of the gene objects on the genome graphic links leads to the relevant Gene record, for example Gene ID: 4512 in the case of COX1.
Try it out using the following example searches and let us know what you think!
On Wednesday, September 11, 2019 at 12 PM, NCBI staff will present a webinar for people with limited experience working with gene and sequence information. You will learn about the kinds of data available for genes and sequences, how to select the most informative records, and how to find related genes and sequences using pre-computed information and the BLAST sequence search service.
- Date and time: Wed, Sep 11, 2019 12:00 PM – 12:30 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
We are now showing the curated evidence used for assigning names and, if possible, gene symbols, publications, and Enzyme Commission numbers on nearly 70% (83 million) microbial RefSeq proteins. This evidence includes a hierarchical collection of curated Hidden Markov Model (HMM)-based and BLAST-based protein families, and conserved domain architectures.
We recently showed you a new a way to search for and view sets of orthologous genes from vertebrates. You can now get an additional set of search results that we are calling similar genes. These are related through protein architecture to the orthologous gene set and include genes from all metazoans and selected plant, fungal, and protist species. You can quickly find related genes within a species, compare them to those from other annotated metazoan genomes, and have access to other useful gene resources. To find a set of similar genes, enter a gene symbol or select the gene symbol + orthologs option from the selections menu.
For example if you search for ‘AGO2 orthologs‘, in addition to the link to orthologs from vertebrates, you’ll get a link to a set of similar genes (Genes with similar protein architectures) across a broad evolutionary spectrum that includes genes from invertebrates, fungi, and green plants (Figure 1).
Figure 1. Genes with similar protein architectures to AGO2. The original search was AGO2 orthologs, which brings up the suggestion box with the links to similar genes as well as the AGO2 vertebrate orthologs. The similar genes include entries from a broad taxonomic range of eukaryotic organisms.
If you search for ‘GH1‘, you’ll get a link to similar genes that includes members of the growth hormone family that are not part of NCBI’s vertebrate ortholog set.
Figure 2. The human subset of genes with similar protein architectures to GH1 showing other members (paralogs) of the GH1 gene family (GH2, CSH1, CSH2, CSHL1). These are not included in the ortholog set.
Try out the following searches and follow the links to the Genes with similar protein architectures
Please let us know what you think!
As you probably know, BLAST has been offering a new results page as an option for standard BLAST for you to test and provide feedback since April. See our post from earlier this spring for more details. We have just added new results pages (Figure 1) for the following four specialized BLAST services for you to test.
- Align two or more sequences
We recently updated the version 5 BLAST protein databases, (dbV5), on our FTP site to be completely accession-based. As we described in a previous post, this means they now contain the gi-less proteins from the NCBI Pathogen Project and other high-throughput projects. The v5 databases are also compatible with proteins from PDB structures with multi-character chain identifiers and will include these as they become available in our other protein systems. Only the latest version of BLAST+ (2.9.0, download) will work with the updated v5 databases and allow you to access all of the most recent protein data. At the end of September 2019, we will stop updating the version 4 BLAST databases and offer the v5 databases as the default for download.
For more information on the new database version and BLAST+ (2.9.0), see the previous NCBI Insights article and the recording of our recent webinar.
NCBI is testing a new way to find and retrieve orthologous vertebrate genes. To find orthologs enter a gene symbol (e.g. RAG1) or a gene symbol combined with a taxonomic group (e.g. primate RAG1). Select the matching entry from the suggestions menu or you can select the orthologs option (e.g. Rag1 orthologs) to see all orthologs. Your search will return a results link to the set of orthologs provided by NCBI’s Gene resource. Click on the results link to see information for that ortholog group (Figure 1).
Figure 1. Search for Rag1 orthologs showing the link to the set of RAG1 genes from vertebrates.
If you’ve been searching in Gene, Nucleotide, Protein, Genome or Assembly databases, you’ve probably noticed the new search experience we introduced in September to interpret several common language searches and offer improved results. We’re excited to announce we’ve added as-you-type suggestions to the search bar in these databases.
Here’s a peek at the new menu in the NCBI Gene database.
Figure 1. Typing into the search box brings up automatic suggestions of the most popular queries.