Name
SSN
Biochemistry
II Bioinformatics extra credit problem set
Due
April 20th in class. Hand
in your answers to the following questions on this page. You will need to give us feedback about the
web site in order to qualify for extra credit.
Use the links and their instructions from the Applications
section to help answer the following questions. More than one application may need to be used at a time. Hint: Keep all results from the applications open
until problem set is complete, you will most likely need them more than once.
1. (3 pts)Find the most probable origin for the
following protein sequence. Give the name of the gene, the organism it comes
from, and what protein it encodes?
MSSIVNKSGT RFAPKVRPRR AATGGTPTPK PRTPQLFIPE
SKEIEEDNSD NDKGVDENET
AIVEKPSLVG ERSLEPFTLT GTNGHDNEIG DEGPIDASTQ
NPKADVIEDN VTLKPAPLQT
HRDQKVPRSS RLASLSKDNE SRPSFKPSFL DSSSNSNGTA
RRLSTISNKL PKKIRLGSIT
ENDMNLKTFK RHRVLGKPSS SIVSKISPPT AMTDSLDRNE
FSSETSTSRE DENENYVISK
VKDIPKKVRD GESAKYFIDE ENFTMAELCK PNFPIGQISE
NFEKSKMAKK AKLEKRRHLR
ELRMRARQEF KPLHSLTKEE QEEEEEKRKE ERDKLLNADI
PESDRKAHTA IQLKLNPDGT
MAIDEETMVV DRHKNASIEY PRPSYTDPWT VEEMIKFYKA
LSMWGTDFNL ISQLYPYRSR
KQVKAKFVNE EKKRPILIEL ALRSKLPPNF DEYCCEIKKH
HMKEIEEAKN TAKEEDQTAG
RLNDANLNKK GSGGIMTNDL KVYRKTEVVL GTIDDLKRKK
LKERNNDDNE DNEGSEEEPE
IDQ
2. (3 pts)Compare the sequence given in problem
one with the full sequence of the answer to problem one. What percent identity do they share?
3. (3 pts)Using the full amino acid sequence,
determine the DNA sequence of the gene.
How many nucleotides in length is it?
Give the first and last ten nucleotides of the sequence.
4. (3pts)Which of the following restriction
enzymes cut the DNA and at what base pairs, using the complete DNA sequence
from your answer to question 3 (not just the 20 nucleotides you wrote
down).
ApaI, ClaI, EcoRI, BglI, HaeIII.
5. (3pts)Using the literature retrieval links,
find a paper describing a human homologue to this protein, and give a full
citation. (Hint: you may have to use
something other than PubMed)
For you to receive extra
credit, please give us insightful feedback about our web site.
On
a scale of 1 to 5 with five being great, one being needs improvement, please
rate the following:
Overall
web site 1 2 3 4 5
Ease
of use 1 2 3 4 5
Website
Information 1 2 3 4 5
Instructions
for applications 1 2 3 4 5
What
did you find was most informative and helpful about this site?
What
did you find was least informative and helpful about this site?
What
should we change to make the site more interesting and useful to future
students at the University of Colorado?