Name: ____________________
Assignment #1 (due Tuesday, Feb 5 by 5pm)
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 and synthesize the
information. NO, just stating Bioinformatics is not good enough)
Center for Information Biology and DNA Data Bank of Japan
http://www.cib.nig.ac.jp/Welcome.html
European Bioinformatics Institute
http://www.ebi.ac.uk/
National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/
Swiss Institute of Biotechnology
http://www.isb-sib.ch/
The J. Craig Venter Institute
http://www.tigr.org/
2) Within NCBI, go to the “Genomic Biology” site (tab on the left-side) and pick
your favorite organism-specific genome databases. Go to its mapview and
genome project overview links (and other links if necessary) to provide the
following details:
a) the number of chromosomes within the organism,
b) how many maps are available (specify the various types)
c) organizations involved in the genome sequencing projects
d) estimated number of genes or proteins identified.
3) 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 )
and open the find your accession number file next to assignment 1. Record your
accession number 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 pellucida C protein is ZPC; list other synonyms if there are any)
______________
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: _______________