Bioinformatics 1 Exercise 3

Notes

Introduction (Exercise 3)

Cheat sheet (Exercise 3)

Part I – Cloning experiment

1.1	Starting from a given cloning sequence and find out which cloning vector (name, accnr, length) was used (e.g. using the tool VecScreen or DDBJ VecScreen).
1.2	Where is the insert in the given sequence located (position from-to, length)?
1.3	Identify the insert (name, accesion number, organism, length, amino acid sequence, function)?
1.4	Determine the restriction enzyme (6bp cutter) used for incorporating the insert (name, sequence).
1.5	Are there homolog proteins in humans (name, accesion number, description, conserved domains)

Part II – Protein 3D structure

2.1	Show 3D protein structure of a homolog human protein (including DNA binding) (from 1.5) and give PDB identification code for this structure.

VecScreen results

VecScreen from cloning sequence

Blastn against Nucleotide collection (nr/nt)

Blastp against human Refseq database