Name: ____________________
Assignment #1 (due Friday, Sept 11 by midnight)
1) Go the organizations listed below and “surf” them. Answer the following
questions:
Central question:
In your own words, what is the mission or role of these bioinformatics-related
organizations? Also, answer any other questions listed under the sub-headings.
a) Center for Information Biology and DNA Data Bank of Japan
http://www.cib.nig.ac.jp/Welcome.html
(note: not looking for too much detail here, just a brief synopsis of their
mission/role)
b) European Bioinformatics Institute
http://www.ebi.ac.uk/
i) mission/role
i) how many countries support the European Molecular Biology Laboratory (EMBL)
ii) how many EMBL facilities are there?
c) National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/
i) go to "More about NCBI" listed under "What does NCBI do" and then go
to "NCBI at a Glance" to provide a detailed answer about the mission and
activities at NCBI
d) Swiss Institute of Biotechnology
http://www.isb-sib.ch/
(note: be sure to click on the "About SIB" link directly to get the overview
before you click on sub-topics in the drop-down menu such as "Vision and
Mission" )
e) The J. Craig Venter Institute
http://www.tigr.org/
i) mission/role
i) Briefly describe 3 different projects that this institute is engaged in
2) Within NCBI, go to the “Genomic Biology” site (tab on the left-side) and pick
your favorite non-human eukaryotic genome project (examine the list on the right
within "Organism-Specific"). Go to its mapview and genome project overview
links (and other links if necessary) to provide the following details:
a) What organism did you choose (common and Latin species name)?
b) Describe the chromosome content of this organism have? (e.g.
autosomes vs sex chromosomes; how many chromosomes do they have
with regards to haploid vs diploid; any organelle chromosomes)
b) Which organizations are involved in the genome sequencing projects
3) Everyone in the class has been assigned a protein or DNA accession number.
Go to the class website and open the "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. Also list other
synonyms or names that it goes by. And list the abbreviation (e.g. zona pellucida
3 gene has a synonym which is zona pellucida C, the abbreviation is ZP3)
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 (cds)?
g) What nucleotides within the mRNA correspond to the polyA signal?
h) What is the chromosomal localization of your gene? (Examples: 12q23)
________________
i) What is the functional role of the protein? (hint: you will likely need to search
the literature)
j) What is the RefSeq accession number of the protein ortholog from mouse and
from rat? Mouse: ______________ Rat: _______________