The document discusses hosting a GIT repository on GitHub and accepting an invitation to a shared repository called "Bioinformatics-I-2015" hosted on GitHub.ugent.be. It also lists some example control structures for Python scripts like if/else statements and for loops and poses extra bioinformatics analysis questions that could be answered using Python scripts.

2. FBW
1-12-2015
Wim Van Criekinge

3. GitHub: Hosted GIT
• Largest open source git hosting site
• Public and private options
• User-centric rather than project-centric
• http://github.ugent.be (use your Ugent
login and password)
– Accept invitation from Bioinformatics-I-
2015
URI:
– https://github.ugent.be/Bioinformatics-I-
2015/Python.git

4. Control Structures
if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue

5. Extra Questions (2)
• How many human proteins in Swiss Prot ?
• What is the longest human protein ? The shortest ?
• Calculate for all human proteins their MW and pI, display as
two histograms (2D scatter ?)
• How many human proteins have “cancer” in their description?
• Which genes has the highest number of SNPs/somatic
mutations (COSMIC)
• How many human DNA-repair enzymes are represented in
Swiss Prot (using description / GO)?
• List proteins that only contain alpha-helices based on the
Chou-Fasman algorithm
• List proteins based on the number of predicted
transmembrane regions (Kyte-Doollittle)

6. Primary sequence reveals important clues about a protein
DnaG E. coli ...EPNRLLVVEGYMDVVAL...
DnaG S. typ ...EPQRLLVVEGYMDVVAL...
DnaG B. subt ...KQERAVLFEGFADVYTA...
gp4 T3 ...GGKKIVVTEGEIDMLTV...
gp4 T7 ...GGKKIVVTEGEIDALTV...
: *: :: * * : :
small hydrophobic
large hydrophobic
polar
positive charge
negative charge
• Evolution conserves amino acids that are important to protein
structure and function across species. Sequence comparison of
multiple “homologs” of a particular protein reveals highly
conserved regions that are important for function.
• Clusters of conserved residues are called “motifs” -- motifs
carry out a particular function or form a particular structure
that is important for the conserved protein.
motif

7.  The hydropathy index of an amino acid is a number
representing the hydrophobic or hydrophilic properties of its
side-chain.
 It was proposed by Jack Kyte and Russell Doolittle in 1982.
 The larger the number is, the more hydrophobic the amino
acid. The most hydrophobic amino acids are isoleucine (4.5)
and valine (4.2). The most hydrophilic ones are arginine (-4.5)
and lysine (-3.9).
 This is very important in protein structure; hydrophobic
amino acids tend to be internal in the protein 3D structure,
while hydrophilic amino acids are more commonly found
towards the protein surface.
Hydropathy index of amino acids

8. 5-hydroxytryptamine receptor 2A isoform 1 [Homo sapiens]
NCBI Reference Sequence: NP_000612.1
GenPept Identical Proteins Graphics
>gi|10835175|ref|NP_000612.1| 5-hydroxytryptamine receptor 2A isoform 1 [Homo sapiens]
MDILCEENTSLSSTTNSLMQLNDDTRLYSNDFNSGEANTSDAFNWTVDSENRTNLSCEGCLSPSCLSLLH
LQEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYR
WPLPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGISMPI
PVFGLQDDSKVFKEGSCLLADDNFVLIGSFVSFFIPLTIMVITYFLTIKSLQKEATLCVSDLGTRAKLAS
FSFLPQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICK
ESCNEDVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENKKPLQLILVNTIPALAYK
SSQLQMGQKKNSKQDAKTTDNDCSMVALGKQHSEEASKDNSDGVNEKVSCV

9. (http://gcat.davidson.edu/DGPB/kd/kyte-doolittle.htm)Kyte Doolittle Hydropathy Plot

10. Possible transmembrane fragment

11. Window size – 9, strong negative peaks indicate possible surface regions
Surface region of a protein

13. Prediction of transmembrane helices in proteins
(TMHMM)

14. 5-hydroxytryptamine receptor 2A (Mus musculus)

15. 5-hydroxytryptamine receptor 2 (Grapical output)

16. Examen.py
http://bioinformatics.biobix.be/examen/
Check availability of PC rooms plus additional
dates