Autosuggest comes to Gene, Nucleotide and other databases


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.

"human" is typed in the search box and a drop-down menu shows the most popular results

Figure 1. Typing into the search box brings up automatic suggestions of the most popular queries.

Continue reading

Upcoming Changes to EST and GSS Databases


Update: NCBI is now in the process of merging EST and GSS records into the Nucleotide database, and we expect to complete this process in early 2019. Accession.version and GI identifiers will not change during this process.

As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database. This change will provide a single point of access for all GenBank sequence data with a common look and feel.

Read more to learn about how this change affects these resources:

  • Websites (Entrez)
  • APIs (E-utilities)
  • FTP sites
  • Submission procedures
  • BLAST
  • TSA (have a look if you’re not familiar!)

Continue reading

Sequence Viewer 3.23 now available


Sequence Viewer 3.23 has several new features, improvements and bug fixes, including performance optimization for alignment renderings and improved tooltips in uploaded VCF files. For a full list of changes, see the Sequence Viewer release notes.

Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.

September 2017: NCBI to present EDirect workshop at NLM


On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.

NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.

Continue reading

Sequence Viewer 3.22 now available


Sequence Viewer 3.22 has several new features, improvements and bug fixes, including improved rendering on BAM and cSRA tracks. For a full list of changes, see the Sequence Viewer release notes.

Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.

RefSeq Functional Elements now public


NCBI is pleased to announce the initial data release of RefSeq Functional Elements, a resource that provides RefSeq and Gene records for experimentally validated human and mouse non-genic functional elements. Data can be accessed via GeneNucleotideBLASTBioProjectGraphical Displays and FTP.

Continue reading

Designing exon-specific primers for the human genome


A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.

Here are the steps to follow to design primers to amplify exon 15 from human BRCA1:

Continue reading