NCBI Minute: A Beginner's Guide to Genes and Sequences at NCBI

Peter Cooper from the NCBI introduces the webinar focused on 'A Beginner's Guide to Genes and Sequences at NCBI.' He mentions the webinar was prompted by librarians at Fanshawe College in Canada who were seeking guidance on using NCBI for sequence research. Cooper emphasizes the importance of understanding how NCBI works, given the gaps in people's knowledge. He plans to spend most of the time on live demonstrations, covering topics from gene and sequence representation at NCBI to the use of traditional search systems and tools like Entrez and BLAST. Cooper also introduces a new search experience on the NCBI site that streamlines the search across different databases.

The speaker discusses how NCBI represents the central dogma of molecular biology, starting from DNA, through RNA splicing, to protein formation. He uses the APRT gene as an example, showing its representation in the NCBI genome browser with its two transcript variants and corresponding protein isoforms. The paragraph also covers the source of sequences at NCBI, including GenBank and the NCBI Reference sequences. It highlights the different types of sequences available for the APRT gene, such as transcripts, proteins, and genomic sequences, and touches on the connection to structural data via the PDB database.

The paragraph explains the traditional search methods at NCBI, using the Entrez text system and the BLAST sequence similarity search system. It points out the challenges of searching across different databases and silos. The speaker then introduces the new search experience, which provides a more streamlined and Google-like interface, allowing users to search without knowing the specific database. The paragraph also demonstrates how to find the APRT gene and its related sequences using the new search features, including the Orthologs button for finding related proteins and sequences.

The speaker delves into the reference sequences for the APRT gene, showing how to find and work with splice variants and the RefSeq Select project for representative transcripts. He also guides on finding related sequences in other organisms using the Orthologs button and the 'Genes similar to APRT' link for a broader range of sequences. The paragraph includes a demonstration of adding sequences to a cart and using the protein alignment tool, COBALT, to compare selected sequences from different organisms.

The paragraph focuses on using BLAST for searching and aligning sequences. It demonstrates how to download sequences and use BLAST to find closely related organisms. The speaker also shows how to perform a BLAST search with nucleotide sequences and discusses the significance of BLAST results, including E-values and the importance of selecting the appropriate database for the search. The paragraph concludes with a brief mention of traditional BLAST searches to find bacterial transferases and examine their structures.

The speaker guides through accessing protein structures from BLAST results and using the iCn3D viewer to examine the three-dimensional structure of the APRT protein. He highlights the ability to view functional sites, such as the active site, and how these sites are conserved across different organisms. The paragraph emphasizes the journey from sequence to the folded protein structure and the availability of functional information within the viewer.

The final paragraph addresses questions from the audience, such as linking PubMed to data and vice versa, the distinction between data reuse and data discovery, and how to find specific types of sequences like ESTs within the nucleotide database. The speaker also provides information on where to find additional resources and assistance, including the NCBI blog, Learn page, fact sheets, and YouTube channel. The webinar concludes with an invitation for further questions and thanks to the participants.