The videos below and corresponding description (including timeline of contents) were found by Kyle Peppler, an undergraduate microbiology major who worked with the Health Science Center Library on a bioinformatics internship funded by Smathers Libraries' internship program. For questions regarding the videos contact Kyle at firstname.lastname@example.org.
This video demonstrates the use of NCBI web resources and Edirect Unix command interface for retrieval of gene sequence information
Timeline of contents
Organism(s) in which the information in the database was derived: Humans, plants, insects, marine life, etc.
The NCBI Gene database is a one-stop location for obtaining gene information including sequence, transcripts, proteins, and expression levels by tissue. It links to other NCBI as well as external resources for identifying sequence similarity, genetic variations, population genetics, etc.
Timeline of contents:
Using the EME1 gene (involved in DNA repair) as an example, this video demonstrates
Organism(s) in which the information in the database was derived: Humans, plants, insects, and marine life, etc. Refer to https://www.ncbi.nlm.nih.gov/gene/statistics/ for a complete list
Organism(s) in which the information in the database was derived: This database houses the genetic information on numerous viruses, such as a DNA virus or retro virus. For a complete list, please refer to https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239
Ensembl houses genomic information for a variety of organisms. Ensembl features many of the tools found on the NCBI Gene database, such as viewing of gene structure (i.e. introns and exons). In Ensembl, sequences can be downloaded in two different file extensions: FASTA and RTF. Ensembl is hosted by the European Bioinformatics Institute.
This video uses the human BRCA2 gene (a tumor suppressor gene) as an example search and demonstrates
Organism(s) in which the information in Ensembl was derived include
A full list of available organisms can be found in the dropdown box on the Ensembl site found at the following link: https://useast.ensembl.org/info/about/species.html
EuPathDB is a family of databases that house genetic information (sequence, variation, orthologs) on various types of pathogens.
This video uses EuPathDB’s CryptoDB database as an example. Other databases housed within EuPathDB share the same interface. The video discusses
Organism(s) in which the information in a database was derived: This database houses genetic information on various pathogens such as the following:
viruSITE houses genomic and proteomic information for a range of viruses. Data from viruSITE are extracted from NCBI RefSeq, Uniprot Knowledgebase (UniprotKB), ViralZone, and PubMed. This database is maintained by the Institute of Molecular Biology at the Slovak Academy of Science. You can access viruSITE through its URL http://www.virusite.org/.
The video above introduces to us the general layout and the type of information that we can find in a viruSITE record. Using the human herpesvirus 7 as an example
The following two videos focus on viruSITE features that allow for the identification of sequence similarity and protein domains. Protein domains are blocks of conserved amino acids among similar proteins that are essential to protein function.
The video above shows how to identify similar sequences in viruSITE from a query nucleotide or amino acid sequence. viruSITE presents results by either listing proteins that are similar to the query sequence or viruses whose genome in which the query sequence can be found. This video was published on 3/29/2016 and is 3 minutes 23 seconds in duration.
The above video addresses methods to
viruSITE also allows us to browse by taxon using a taxonomy browser and the video that demonstrates how to do this is below
Similar to NCBI and Ensembl, the virusSITE contains an interactive genome browser and the video posted below shows how to use this feature of the viruSITE database
The UCSC Genome Browser is a comprehensive genome database that allows users to accesses graphical models of genes, gene expression, epigenetic (i.e. histone modifications), genetic variants information. The following videos were published by Katherine West at the University of Glasgow in March, 2018 and thus represent some recent tutorials for the use of the UCSC Genome Browser.
The introductory video above discusses the following
The second video in the series is listed above and it shows how to
The third video in the series found above demonstrates how to view gene expression data.
The last video in this series is found above and demonstrates how to view epigenetic information such as histone modifications in genes.