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Introduction to Bioinformatics Databases - 2014

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Robert Wright

on 12 November 2015

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Transcript of Introduction to Bioinformatics Databases - 2014

Gene
Reference Sequences (RefSeqs) are non-redundant and richly annotated sequences representing naturally occurring molecules of DNA, RNA, and protein.

OMIM
OMIM?
Disorders/
Gene?
HomoloGene
An Introduction to
Bioinformatics Databases:
OMIM, Gene, & HomoloGene

Welch Medical Library
6/19/14
NCBI
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).
Multi-Search
http://www.ncbi.nlm.nih.gov/
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.
http://nar.oxfordjournals.org/content/41/D1/D8.full.pdf
http://www.ncbi.nlm.nih.gov/HomoloGene/HTML/Overview.html
HomoloGene?
Genes
Access from (1) NCBI's GQuery,
(2) OMIM.org's basic search or
(3) OMIM.org's advanced search
records
OMIM ...
clinical
Links to
related
in
... including
features
Link
to
associated
gene/locus
What
is
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.
Clinical Synopsis
http://www.omim.org/
Access from (1) OMIM.org's basic search,
(2) the Gene Map Advanced Search,
or (3) other OMIM.org records
Link
to
a
chromosome
map
view
Link
to
the
UCSC
Genome
Browser
®
Gene records link to a variety of databases, within and outside of NCBI
http://www.ncbi.nlm.nih.gov/gene
What
is
Gene annotations include genomic regions, transcripts, products, phenotypes,
interactions, pathways, etc.
homologous genes,
protein sequence records,
SNPs, etc.
for information on
Gene
Access from (1) Gene's basic search,
(2) Gene's advanced search,
or (3) links from OMIM
Records
in
1
2
3
Access
Method
Access
Method
Access
Method
The Gene advanced search keeps track
of your search history. You can combine
multiple searches from your search history
to form a new query.
(via OMIM)
the
Sequence
Viewer
Using
Using
the
Map
Viewer
What
is
NCBI?
It supports research in computational biology, develops software tools for sequence analysis,
public
bioinformatics
databases.
and
creates
&
maintains
Questions?
Please
contact
us!
Peggy Gross
Rob Wright
mgross21@jhmi.edu
rwrigh32@jhmi.edu
Similar to a review article, a RefSeq is a
synthesis of information integrated across
multiple sources
(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.
http://www.ncbi.nlm.nih.gov/books/NBK21091/
Hover over tracks to get overview descriptions,
explanations of track graphics, and the option to
hide tracks.
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.
Use the
"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.
What
is
Finding
Orthologs
(homologous sequences in different species)
Click on "hm" in the Map Viewer to discover homologs to GNAQ in HomoloGene.
Resources
OMIM Tutorial
NCBI Tutorials
NCBI Discovery Workshops
Sources
&
http://www.ncbi.nlm.nih.gov/homologene
http://www.openhelix.com/OMIM
http://www.youtube.com/ncbinlm
http://www.ncbi.nlm.nih.gov/education/workshops/
®®
®
®
®
®®
®®
®
(Online Mendelian Inheritance in Man)
®
®
genes
phenotypes.
GQuery
Phenotypes
Because "-" is used to exclude terms, don't use hyphenated keywords in your search.
Today's Agenda

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
Full transcript