1. Introduction to Bioinformatics
Part 2 of 2
M.E:
September 8, 2003
Jonathan Pevsner, Ph.D.

2. Copyright notice Many of the images in this powerpoint presentation
are from Bioinformatics and Functional Genomics
by Jonathan Pevsner (ISBN ).
Copyright © 2003 by John Wiley & Sons, Inc.
These images and materials may not be used
without permission from the publisher. We welcome
instructors to use these powerpoints for educational
purposes, but please acknowledge the source.
The book has a homepage at
Including hyperlinks to the book chapters.

3. We posted 1000 bioinformatics links here:
then click “bioinformatics”

4. Question #3:
How can I use NCBI
(or other sites)
to find information
about a protein
or gene?

5. Four ways to access protein and
DNA sequences
[1] LocusLink with RefSeq
[2] Entrez
[3] UniGene
[4] ExPASy Sequence Retrieval System
(this is separate from NCBI)

6. 4 ways to access protein and DNA sequences
[1] LocusLink with RefSeq
LocusLink is a great starting point: it collects
key information on each gene/protein from
major databases. It now covers 8 organisms.
RefSeq provides a curated, optimal accession number for each DNA (NM_006744)
or protein (NP_007635)
[2] Entrez
[3] UniGene
[4] ExPASy SRS

7. What is an accession number?
An accession number is label that used to identify a sequence. It is a string of letters and/or numbers that corresponds to a molecular sequence.
Examples (all for retinol-binding protein, RBP4):
X GenBank genomic DNA sequence
NT_ Genomic contig
Rs dbSNP (single nucleotide polymorphism)
N An expressed sequence tag (1 of 170)
NM_ RefSeq DNA sequence (from a transcript)
NP_ RefSeq protein
AAC02945 GenBank protein
Q SwissProt protein
1KT7 Protein Data Bank structure record
DNA
RNA
protein

11. 4 ways to access protein and DNA sequences
[1] LocusLink with RefSeq
[2] Entrez
Entrez is divided into sites for nucleotide, protein,
structure, genomes, OMIM, and more. You can use limits
(such as RefSeq) to focus your Entrez search.
[3] UniGene
[4] ExPASy SRS

17. FASTA format

18. Graphics format

19. 4 ways to access protein and DNA sequences
[1] LocusLink with RefSeq
[2] Entrez
[3] UniGene
UniGene collects expressed sequence tags (ESTs)
into clusters, in an attempt to form one gene per cluster.
Use UniGene to study where your gene is expressed
in the body, when it is expressed, and see its abundance.
[4] ExPASy SRS

20. 4 ways to access protein and DNA sequences
[1] LocusLink with RefSeq
[2] Entrez
[3] UniGene
[4] ExPASy SRS
There are many bioinformatics servers outside NCBI.
Try ExPASy’s sequence retrieval system at
(ExPASy = Expert Protein Analysis System)
Or try ENSEMBL at for a premier
human genome web browser.

21. Question #4:
How can I find
information about
a particular disease?
Answer:
Try OMIM

24. Two main disease databases: general and locus-specific
OMIM
GeneCards (Weizmann)
Genes & Disease (at NCBI)
Locus-specific
Human Gene Mutation Database (HGMD)

27. Course sponsors Dean’s Office, School of Medicine
Division of Health Sciences Informatics
Welch Medical Library
Kennedy Krieger Institute
Dept. of Neuroscience
Dept. of Biostatistics, School of Public Health