Seminar&workshop Bioinformatica 18 okt 2011
Workshop Databases and algorithms
Part1

Skills: Blast, alignment and database browsing
Given human protein sequence:
MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ
CPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKD
EVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYI
ELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQ
1) Use the appropriate database to find your protein(ID)
Protein name: …………………………
uniprotID:……………………………….
refseqID:…………………………………
2) Find its homolog in M.musculus by using the databases, give its refseqID and explain the
prefix of this ID
refseqID mouse homolog: ………………………..
ID prefix means: ………………………………………
3) Make an alignment of the human and mouse using an online tool (e.g. clustalW). Download
the alignment file (e.g. .aln, clustalW format)
4) Look for the 3D protein structure of the protein (H.sapiens) find out which known protein
domains you can find within this protein by using the appropriate database. Give three.
i)
……………………………..
ii)
……………………………..
iii)
……………………………..
Part 2

Skills: SNP database/genome browsing, OMIM database
Sickle cell anemia is caused predominantly by a specific mutation in the HBB gene. The
mutant is called Hbs.
1)Locate the HBB gene on the genomic map below:
2) Write down the first ten amino acids of the HBB protein and the Hbs mutant. Within you
should find a difference in amino acid code, caused by the mutation in the gene. Make use of
the NCBI SNP and OMIM database. What is the genomic position (bp) of the mutation
according to het Huref genome sequence?
SNPdb ID: …………………………
HBB
Hbs
Position on the genome (Huref):……………………