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MOLECULAR BIOLOGY EXERCISE SESSION (EVOLUTIONARY TREE – PRIMERS –…
MOLECULAR BIOLOGY
EXERCISE SESSION
EVOLUTIONARY TREE – PRIMERS – HUMANPROTEINATLAS
EX. 6
Phylogenetic analysis
for the non-
specialist
primer design for PCR
tool
HUMAN PROTEIN
ATLAS
PROTEIN STRUCTURE
EX. 1
how to use the
DeepViewSwiss-PdbViewer
protein
database
pdb format files
structural
characteristics
primary structure
secondary structure
H bonds
ternary structure
Cystein group - disulfide bridge
Active site of enzyme
oligomeric
proteins
DOTPLOT – PAIRWISE & MULTIPLE ALIGNMENT
EX. 3
DOTPLOT
:
Use IE, Firefox or Safari
Making repeats visible
Make introns/exons visible
PAIRWISE ALIGNMENT
links for tools = look at ex. document.
MULTIPLE ALIGNEMENT: CLUSTAL X
DATABASE
EX. 2
databases
containing biological information
NCBI
Genome Data Viewer (look in Genomes and Maps)
OMIM (Online Mendelian Inheritance in Man)
NCBI > Genomes and maps >
Genome
NCBI GLOBAL CROSS-DATABASE
SEARCH
Also search by choosing the right database
Advanced search
The use of Index list function
history function
EXPERT PROTEIN ANALYSIS SYSTEM
EXPASY
protein sequences and
structures as well as 2D PAGE
UniPROT
protein sequence and functional information.
PROSITE
database (containing protein sequence motifs).
THREE DIMENSIONAL STRUCTURE
[PDB file database]
(
http://www.rcsb.org/pdb/home/home.do
)
BLAST
EX. 4
NCBI BLast
tools
GENE PREDICTION, PROTEIN CLASSIFICATION
EX. 5
NCBI ORF
finder
Protein classification
primary structures
secondary structures
ternary/quaternary structure
Databases (look at the ex. document)
genscan