1. 2011 edition: Genomic pyramids

2.  The human genome is a 3bln character string of
nucleotides: [ACTG]{3000000000}
 Next-generation sequencing allows the genome to be
sequenced at low costs in a short term
 For example 454 sequencing generates >1mln 400bp
sequences
 Homopolymer problems! Observed vs expected homopolymer
12
length
10
Fluorescence Observed
Expected
8
6
4
2
0
0 2 4 6 8 10 12
Homopolymer size

3.  Define a homopolymer block AAAA starting on
position 10 as 10A4
 Position = 10
 Nucleotide = A
 Altitude = 4
 ACGTAGGTTTCCA
Genomic pyramid
1 1 1 1 1 2 3 2 1
 Start=5; Stop=13; Surface=9; Height=3; Width=5

4.  Genomic pyramids
 Have a peak of at least 3 high 121
 Are bordered by a 1 left and a 1 right 23432
 Have a minimal width of 5 1231
 Do NOT have to be symmetric 123431
 Do NOT have ‘a local minimum’ 1235341
 Do NOT overlap with another pyramid 12321231
 Examples of good pyramids:
 1 2 3 2 1, 1 2 5 4 3 2 1, 1 2 5 3 1, 1 3 5 4 3 1 …
 Each pyramid has a start position, a stop, a height, a
width and a surface

5.  You are given:
 The complete human genome sequence @
http://athos.ugent.be/BPC/genome (be gentle on the
server when downloading…)
 Chromosome Y contains 27744 pyramids , biggest=45
highest=38 widest=7
 You are asked to give:
 The highest, the widest and biggest surface pyramid in
the human genome by the start position
 In case of a draw, give the number of ‘draw pyramids’

6.  In case the previous questions were not exactly
difficult enough, answer the following
 Is there a gene or (multiple genes) that overlaps with 2 of
the 3 special pyramids (biggest, widest, highest). If so,
give the name(s) of the gene(s)
 Given that π is 3.1415, we define πramids as 3 consecutive
genomic pyramids(start locations) that are spaced a
multiple of 14 and 15 apart on the same chromosome.
How many πramids can you find? In which genes?
Δ ---- x*14 ---- Δ ---- x*15 ---- Δ
Δ ---- x*14 ---- Δ Δ Δ ---- x*15 ---- Δ
Δ - 10 - Δ – 18 -Δ ---- x*15 ---- Δ

7.  You are allowed to work together, but submit results
individually
 Submit your final (partial) answers (!= questions) to
joachim.deschrijver@ugent.be
 Questions? After the practicum exercises @ Thursday
 Submission deadline: 2011
 The winner receives
 A place in the FBW Bioinformatics Hall of Fame
 Life long respect and recognition :-)
 Life long free linux (web)hosting
 … a secret prize

8.  Enjoy !
 Don’t crash your computer!
 Don’t waste computing time
and/or memory:
CODE EFFICIENT