1. The International Nucleotide Sequence Database Collection (INSDC) synchronizes their
sequence records on a daily basis. For the GenBank sequence of human alpha globin sequence,
find the corresponding sequence records in EMBL and DDBJ. Comment on the formats used by
the three databanks and if all the features in the GenBank entry are integrated into the other
databases.
Comments on the formats used by the three databanks for the corresponding sequences:
GeneBank:
EMBL:
DDBJ:
I could not retrieve any data from here: DDBJ.
2. Use the PubMed to search for articles that describe gene detection algorithms using neural
networks. Name some journals that publish articles in bioinformatics.
Some journals that publish articles in bioinformatics include:
 Bioinformatics
 BMC Bioinformatics
 PLOS Computational Biology
 Briefings in Bioinformatics
 Journal of Computational Biology
 IEEE/ACM Transactions on Computational Biology and Bioinformatics
Here is some of the journals searched in the PubMed website:
3. Obtain information provided on BRC2 protein, implicated in susceptibility to breast cancer,
from the SWISS-PROT database (http://www.expasy.org/sprot/). How many different
sequences of this protein are provided? Comment on how they are different.
In summary, there is only one sequence of the BRC2 protein provided in the SWISS-PROT
database. This is because the BRC2 protein is a specific protein with a unique sequence. However,
there may be different variants of the protein due to genetic variations or post-translational
modifications. The SWISS-PROT entry provides information on these variants and their functional
implications.
4. Perform the same analysis on the haemoglobin protein as you did in the question 3 above. This
time use the PIR database. Also, run these searches on the UniProt (http://www.uniprot.org/). Do
you find any significant enhancements in the information provided by UniProt?
According to the PIR database, there are multiple entries for the hemoglobin protein, including
entries for different species and variants of the protein. The entries provide information on the
protein's sequence, function, structure, and post-translational modifications. They also include
information on the gene, disease association, and related proteins.
PIR database provides more comprehensive information on the hemoglobin protein compared to
the UniProt database. The PIR entries include information on the protein's ontology, domains, and
motifs, as well as its function, structure, post-translational modifications, and interactions with
other proteins. They also provide information on the gene, disease association, and related proteins.
In addition, the PIR database includes links to other databases and resources, such as the Protein
Data Bank (PDB) and the Gene Ontology (GO) database.
5. Retrieve the 3D structure of bovine rhodopsin (a GPCR) from the PDB database (pdb:
http://www.pdb.org). How many entries can you find? Have a closer look at the entry with the best
crystallographic resolution for the complete protein. At what temperature was the crystallization
carried out and how many cysteine bonds does the protein have?
6. In how many assays was the molecule Fenbendazole tested and in how many of these was it
active? What is Fenbendazole used for and how does the molecule differ from Albendazole? Use
the PubChem database (http://pubchem.ncbi.nlm.nih.gov/) to answer this question.
Fenbendazole presents a wide spectrum
anthelmintic effect. It is used against a number
of gastrointestinal parasites including giardia,
roundworms, hookworms, whipworms, and
the Taenia genus of tapeworms, pinworms,
aelurostrongylus, paragonimiasis, strongyles,
and Strongyloides. Fenbendazole is approved
to be administered under veterinary to sheep,
cattle, horses, fish, dogs, cats, rabbits and seals.
It has 36 active substance count when browse
in PubChem database.
Albendazole is an anti-parasitic prescription medicine approved by the U.S. Food and Drug
Administration (FDA) for the treatment of
two parasitic infections: neurocysticercosis
and hydatid disease. Albendazole is also used
to
treat
a
parasitic
infection
called
microsporidiosis. Microsporidiosis can be an
opportunistic infection (OI) of HIV.It has 145
active substance count when browse in
PubChem database.