P6 2017 biopython2

FBW
28-11-2017
Wim Van Criekinge

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

Lists
• Flexible arrays, not Lisp-like linked
lists
• a = [99, "bottles of beer", ["on", "the",
"wall"]]
• Same operators as for strings
• a+b, a*3, a[0], a[-1], a[1:], len(a)
• Item and slice assignment
• a[0] = 98
• a[1:2] = ["bottles", "of", "beer"]
-> [98, "bottles", "of", "beer", ["on", "the", "wall"]]
• del a[-1] # -> [98, "bottles", "of", "beer"]

Dictionaries
• Hash tables, "associative arrays"
• d = {"duck": "eend", "water": "water"}
• Lookup:
• d["duck"] -> "eend"
• d["back"] # raises KeyError exception
• Delete, insert, overwrite:
• del d["water"] # {"duck": "eend", "back": "rug"}
• d["back"] = "rug" # {"duck": "eend", "back":
"rug"}
• d["duck"] = "duik" # {"duck": "duik", "back":
"rug"}

Regex.py
text = 'abbaaabbbbaaaaa'
pattern = 'ab'
for match in re.finditer(pattern, text):
s = match.start()
e = match.end()
print ('Found "%s" at %d:%d' % (text[s:e], s, e))
m = re.search("^([A-Z]) ",line)
if m:
from_letter = m.groups()[0]

Install Biopython
pip is the preferred installer program.
Starting with Python 3.4, it is included
by default with the Python binary
installers.
pip3.5 install Biopython
#pip3.5 install yahoo_finance
from yahoo_finance import Share
yahoo = Share('AAPL')
print (yahoo.get_open())

Prelude
• Erdos
• Gaussian - towards random
DNAwalks
• Fetch random Protein
• AAindex parser

To be adapted for proteins …

Exceptions
• Exceptions are events that can modify the
flow or control through a program.
• They are automatically triggered on errors.
• try/except : catch and recover from raised
by you or Python exceptions
• try/finally: perform cleanup actions
whether exceptions occur or not
• raise: trigger an exception manually in
your code
• assert: conditionally trigger an exception
in your code

Exception Roles
• Error handling
– Wherever Python detects an error it raises
exceptions
– Default behavior: stops program.
– Otherwise, code try to catch and recover from the
exception (try handler)
• Event notification
– Can signal a valid condition (for example, in
search)
• Special-case handling
– Handles unusual situations
• Termination actions
– Guarantees the required closing-time operators
(try/finally)
• Unusual control-flows
– A sort of high-level “goto”

BioPython
• Make a histogram of the MW (in kDa) of all proteins in
Swiss-Prot
• Find the most basic and most acidic protein in Swiss-Prot?
• Biological relevance of the results ?
From AAIndex
H ZIMJ680104
D Isoelectric point (Zimmerman et al., 1968)
R LIT:2004109b PMID:5700434
A Zimmerman, J.M., Eliezer, N. and Simha, R.
T The characterization of amino acid sequences in proteins by
statistical
methods
J J. Theor. Biol. 21, 170-201 (1968)
C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02
5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96

Extra Questions
• 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)

Biopython AAindex ? Dictionary
Hydrophobicity = {A:6.00,L:5.98,R:10.76,K:9.74,N:5.41,M:5.74,D:2.77,F:5.48,
C:5.05,P:6.30,Q:5.65,S:5.68,E:3.22,T:5.66,G:5.97,W:5.89,
H:7.59,Y:5.66,I:6.02,V:5.96}
from Bio import SeqIO
c=0
handle = open(r'/Users/wvcrieki/Downloads/uniprot_sprot.dat')
for seq_rec in SeqIO.parse(handle, "swiss"):
print (seq_rec.id)
print (repr(seq_rec.seq))
print (len(seq_rec))
c+=1
if c>5:
break

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)

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

 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

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

Possible transmembrane fragment

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

Prediction of transmembrane helices in proteins
(TMHMM)

5-hydroxytryptamine receptor 2A (Mus musculus)

5-hydroxytryptamine receptor 2 (Grapical output)

P6 2017 biopython2

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