As you may know, we have been offering a new BLAST results (Figure 1) as a test page since April. In response to your positive reception and after incorporating many improvements that you suggested, we made the new results the default today, August 1, 2019.
You will still be able to access to the traditional results for a several months. This will provide you additional time if you need it to adjust your workflows or teaching materials to the new display.
Thank you for the feedback on the new results. We made several improvements to address issues or concerns that you pointed out. You also told us about 17 additional features you would like us to add. We are working on incorporating these into the page and welcome additional suggestions. Please let us know what you think.
Figure 1. The new BLAST results with filters directly on the page and a more concise tabbed output that includes the taxonomy report. The link at the upper right (circled) retrieves the traditional BLAST results.
In July 2018, NCBI announced plans to retire the EST and GSS databases, and we have now implemented these changes. We will continue to accept submissions of EST and GSS sequences, but will no longer provide special processes for these sequence types. If you want to submit EST and GSS data, please use tbl2asn. For further details, please visit https://www.ncbi.nlm.nih.gov/genbank/dbest/ or https://www.ncbi.nlm.nih.gov/genbank/dbgss/ or contact firstname.lastname@example.org.
We thank all past and present submitters of EST and GSS data for the invaluable benefit these data have provided to numerous genomic sequencing projects over the years. Please let us know if you have any questions or concerns about these changes!
Primer-BLAST, NCBI’s primer-designer and specificity-checker, now offers a way to help you with irrelevant off-target matches.
Sometimes Primer-BLAST can’t design specific primers for your target sequence because of similar non-target sequences in the database. In some cases, you may know that these non-target matches are not important your research and are safe to ignore. Examples may include tissue-specific splice variants, redundant entries, and predicted sequences. To help in these cases, you can now choose to allow certain off-target matches. This gives Primer-BLAST greater freedom in primer selection and a better chance of finding highly specific primers.
The Genome Workbench team is proud to present version 2.13.0, with the latest usability improvements and bug fixes. See the full list of changes in the Genome Workbench release notes.
Some of the improvements include:
- New SNP tracks using the most recent dbSNP release
- Improved alignment statistics table to correctly account for introns
- Alignment tooltips report introns separately from gaps
- Fixes for several interface issues to make MAFFT and BLAST alignments easier to use.
Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse and import data from NCBI and combine it with your own private data.
In late May, we introduced a new type of search experience in NCBI Labs that uses natural language queries to make common tasks easier. The experience at NCBI Labs – where we experiment with potential new features and tools – proved successful. We’re pleased to announce that we added this simplified search capability to NCBI’s global search page. Some natural language queries now work in the “All Databases” search from the NCBI home page!
We know it’s not always easy to find the sequence data you’re after at NCBI. Maybe it’s because you’re no expert at constructing queries, and you end up with no results or too many results. Or maybe you’re an Entrez wizard, but creating a query full of Booleans and filters seems like overkill when you could just write a short natural language query, like you’re used to doing in Google. The next time you search for a gene, transcript or genome assembly for a given organism, try the new search experience we’re piloting in NCBI Labs.
In NCBI Labs, you can now search for sequences using natural language and get the best results.
Figure 1. The new interface for specified transcript search.
The improved search experience now available in NCBI Labs addresses 3 types of queries that commonly fail in searches at NCBI: organism-gene (e.g. human BRCA1), organism-transcript (e.g. Mouse p53 transcripts) and organism-assembly (e.g. dog reference genome). For each of these query types in NCBI Labs, we now return NCBI’s highest quality sequence sets or reference and representative assemblies in an easy-to-view panel.
Example queries are shown below to get you started.
A paper in the January 2018 issue of Database describes the NCBI BioCollections database, a curated dataset of metadata for culture collections, museums, herbaria and other natural history collections connected to sequence records in GenBank. The BioCollections database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows back-linking from the home institution for quick identification of all records originating from each collection.
The rapidly growing set of GenBank submissions frequently includes records that are derived from specimen vouchers. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses.
New repository records are added to the database if they are submitted to the International Nucleotide Sequence Database Collaboration (INSDC) along with sequence data. Each record now provides information about the institution that houses the collection, standard Institution Code, mailing address, and associated webpage if available.
The BioCollections database is maintained and curated by the Taxonomy group at NCBI.
UniVec, NCBI’s non-redundant database of vector sequences, has been updated to build 10.0, which enables searches run using NCBI’s VecScreen tool to detect more of the foreign sequences introduced during the cloning or sequencing process. UniVec build 10.0 is also available via FTP.
This build added 174 complete vector sequences and 214 adapter, primer and other sequences, including 133 RNA Spike-In sequences, bringing the total number of sequences represented in the UniVec database to 3,039.
IgBLAST 1.7.0 release
A new version of IgBLAST is now available on FTP, with the following new features:
- Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
- Set a custom J gene mismatch penalty
- Report the CDR3 start and stop positions in the sub-region table
- Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment.
IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.
The NCBI Multiple Sequence Alignment Viewer (MSAV) is a versatile web application that helps you visualize and interpret MSAs for both nucleotide and amino acid sequences. You can display alignment data from many sources, and the viewer is easily embedded into your own web pages with customizable options. An even simpler way to use MSAV is to use our page, upload your data, and share the link to a fully functional viewer displaying your results.