Name: ____________________
Assignment #1 (due Tuesday, Jan 31)
1) Go the resources below (all five of them) and “surf” them. Answer the
following questions:
a) In your own words, what is the mission or role of the different database
organizations?
b) What is their emphasis of the research performed at these
organizations? (hint: look at their faculty and staff. NO, just stating
Bioinformatics is not good enough)
Resource
DNA Data Bank of
Japan (DDBJ)
European
Bioinformatics
Institute (EBI)
National Center for
Biotechnology
Information (NCBI)
Swiss Institute of
Biotechnology
website
http://www.ddbj.nig.ac.jp/Welcome-e.html
http://www.ebi.ac.uk/
http://www.ncbi.nlm.nih.gov/
http://www.isb-sib.ch/
The Institute for Genomic http://www.tigr.org/
Research (TIGR)
2) Within NCBI, pick your favorite organism-specific genome databases and go
to the link for its Entrez Genome Project website. Provide details on the number
of chromosomes within the organism, how many maps are available, and which
organizations have been involved in the genome sequencing project.
3) Within NCBI, enter “MapViewer” and examine the human genome
chromosomal map. Where does the Melanoma antigen (family A, 2) (MAGEA2)
gene map to? What two genes flank the MAGEA2 gene that are transcribed in
the same direction?
4) Go to the UniGene site within NCBI. In your own words, what is the UniGene
database? Go to your favorite organism in the UniGene database, and find out
how many known genes were identified in the database (as depicted by mRNAs
only). Also, how many total clusters were found within this organism?
5. Everyone in the class has been assigned a protein or DNA accession number. Go to
the class website (http://www.csus.edu/indiv/P/Peavyt/BIOINFO.htm )
to find your accession number. Record it here: _____________
a) Does your accession number refer to an mRNA, Genomic, or protein sequence?
______________
b) What is the name given to your DNA/protein sequence and its abbreviation (e.g. zona
pellucid C protein is ZPC) ______________
c) What species is your protein or DNA from? _________________
d) What is the length of the DNA sequence? ______________
e) How many amino acids are in the protein (in amino acids)? ______________
f) What nucleotides within the mRNA constitute the Coding Sequence?
g) What nucleotides within the mRNA correspond to the polyA signal?
h) What chromosome is your gene localized to? (Examples: 12q23-q24.1, 1q34, etc.)
________________
i) What is the functional role of the protein? (hint: you will need to search the literature)
j) What is the RefSeq accession number of the protein ortholog from mouse and from
rat? Mouse: ______________ Rat: _______________