Oefeningen Bio informatica
Oefenzitting 1
1. The National Centre for Biotechnology Information:
https://www.ncbi.nlm.nih.gov/.
a. Easy access to multiple genomic databases from their
website
b. On which chromosome is a protein located?
c. How many exons?
d. How many of the alcohol dehydrogenase genes of baker’s yeast are
there?
i. (Alcohol dehydrogenase) AND (Saccharomyces cerevisiae)
e. And how many proteins have a length between 50 and 100 AA?
2. Ensemble : http://www.ensembl.org
a. Stores genomic / gene information
b. The best information on genomic information you can find using Ensembl
c. Ensemble ID
d. Search for the genome of Baker’s yeast. Which chromosome is the longest?
e. How many coding genes are there on the human X / Y chromosome?
3. Unitprot : http://www.uniprot.org
a. Stores protein information
b. How many amino acids?
c. What is the amino sequence?
d. Uniprot ID
FYI, yeast: yeastgenome.org, bacteria: ensemblebacteria.org, drosophila:
flybase.org …
Ensemble however links for some organisms’ databases like yeast or drosophila
and that is why you see a weird ensemble ID for the question above.
Oefenzitting 2 + 3
1. RCSB PDB : http://www.rcsb.org/pdb/home/home.do
a. Protein structures; each protein is given a 4 character identifier
b. You can also find more information on the sequence of
the protein, quality parameters and experimental method
on this page. The uniport code (protein database) is also
given. This code can be used to search for the protein in
the NCBI database or the uniprot database.
c. Search for structures determined by EM released between 2010 and
now, how many? Are you observing any trend in the numbers over
the years? Can u suggest why? (this number will increase daily so
you will find different values)
d. What is the identifier of the best resolution structure of canine GDP-
ran?
i. Sort best to worst resolution then check
e. How many 8-bladed beta-propeller are classified in SCOP?
Oefenzitting 1
1. The National Centre for Biotechnology Information:
https://www.ncbi.nlm.nih.gov/.
a. Easy access to multiple genomic databases from their
website
b. On which chromosome is a protein located?
c. How many exons?
d. How many of the alcohol dehydrogenase genes of baker’s yeast are
there?
i. (Alcohol dehydrogenase) AND (Saccharomyces cerevisiae)
e. And how many proteins have a length between 50 and 100 AA?
2. Ensemble : http://www.ensembl.org
a. Stores genomic / gene information
b. The best information on genomic information you can find using Ensembl
c. Ensemble ID
d. Search for the genome of Baker’s yeast. Which chromosome is the longest?
e. How many coding genes are there on the human X / Y chromosome?
3. Unitprot : http://www.uniprot.org
a. Stores protein information
b. How many amino acids?
c. What is the amino sequence?
d. Uniprot ID
FYI, yeast: yeastgenome.org, bacteria: ensemblebacteria.org, drosophila:
flybase.org …
Ensemble however links for some organisms’ databases like yeast or drosophila
and that is why you see a weird ensemble ID for the question above.
Oefenzitting 2 + 3
1. RCSB PDB : http://www.rcsb.org/pdb/home/home.do
a. Protein structures; each protein is given a 4 character identifier
b. You can also find more information on the sequence of
the protein, quality parameters and experimental method
on this page. The uniport code (protein database) is also
given. This code can be used to search for the protein in
the NCBI database or the uniprot database.
c. Search for structures determined by EM released between 2010 and
now, how many? Are you observing any trend in the numbers over
the years? Can u suggest why? (this number will increase daily so
you will find different values)
d. What is the identifier of the best resolution structure of canine GDP-
ran?
i. Sort best to worst resolution then check
e. How many 8-bladed beta-propeller are classified in SCOP?
