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Introduction to Bioinformatics Databases - 2014
Transcript of Introduction to Bioinformatics Databases - 2014
Reference Sequences (RefSeqs) are non-redundant and richly annotated sequences representing naturally occurring molecules of DNA, RNA, and protein.
An Introduction to
OMIM, Gene, & HomoloGene
Welch Medical Library
Our jumping off point ...
The National Center for Biotechnology Information (NCBI) is part of the
National Library of Medicine
at the National Institutes of Health (NIH).
Search simultaneously across more than 30 databases related to human health, genes, proteins, chemicals, etc.
Overviews provide external links to a variety of related genetics resources and references link out to PubMed. Produced by the McKusick-Nathans Institute of Genetic Medicine at the
Provides detailed information for known and predicted genes from all major taxonomic groups.
Includes a multiple sequence alignment tool that compares aligned amino acid sequences between groups of organisms.
An automated system for detecting homologs among the annotated genes of 21 completely sequenced eukaryotic genomes. Information is drawn from sources including OMIM, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database, and FlyBase.
Access from (1) NCBI's GQuery,
(2) OMIM.org's basic search or
(3) OMIM.org's advanced search
A comprehensive, authoritative compendium of human
and genetic Provides full-text, referenced
overviews of all known mendelian disorders and over 12,000 genes.
Johns Hopkins University
School of Medicine.
Access from (1) OMIM.org's basic search,
(2) the Gene Map Advanced Search,
or (3) other OMIM.org records
Gene records link to a variety of databases, within and outside of NCBI
Gene annotations include genomic regions, transcripts, products, phenotypes,
interactions, pathways, etc.
protein sequence records,
for information on
Access from (1) Gene's basic search,
(2) Gene's advanced search,
or (3) links from OMIM
The Gene advanced search keeps track
of your search history. You can combine
multiple searches from your search history
to form a new query.
It supports research in computational biology, develops software tools for sequence analysis,
Similar to a review article, a RefSeq is a
synthesis of information integrated across
(NCBI - GenBank, the European Nucleotide Archive, and the DNA Databank of Japan)
at a given time.
They are generated to provide reference standards for multiple purposes ranging from genome annotation to reporting locations of sequence variation in medical records.
Hover over tracks to get overview descriptions,
explanations of track graphics, and the option to
Use the zoom feature
to see more genes.
Click on track features to view detailed information (e.g. SNP records and PubMed citations)
Use the "Configure" feature to select and reorder tracks.
Use the "Tools" feature to flip strands, set markers, and view sequence as text.
"Maps & Options"
feature to select
& reorder tracks.
Click on the minus signs to remove map tracks. The screen shots that follow show only the Gene map track.
Click on the map to activate
the zoom feature.
Click to download the sequence
of a specific region of interest.
(homologous sequences in different species)
Click on "hm" in the Map Viewer to discover homologs to GNAQ in HomoloGene.
NCBI Discovery Workshops
(Online Mendelian Inheritance in Man)
Because "-" is used to exclude terms, don't use hyphenated keywords in your search.
1. Bioinformatics Portal Overview
2. NCBI/GQuery Overview
3. OMIM Overview
4. OMIM Activity
5. Gene Overview
6. Gene Activity (Genome Workbench)
7. HomoloGene Overview
8. HomoloGene Activity (Mega)
9. Cn3D Activity
10. Specific Cases/Questions