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My master thesis.
I finished my Master Thesis titled
Unique factors in the human genome in
April 2005. Here is the presentation I gave (in
Dutch). And here is a short presentation I gave on
the same subject (in English).
My supervisors were Peter E. M. Taschner (of the
LUMC
Bioinformatics Support Group),
Hendrik Jan Hoogeboom and
Walter A. Kosters.
Many techniques in Bioinformatics use unique strands of DNA. Techniques like
MPLA, PCR and micro arrays all profit from the unicity of markers. We have
made a program suite that implements the following:
- comb: Convert fasta input files to binary, also reserves space
for the output of the mpass program.
- dcomb: Convert binary files back to ASCII.
- mpass: Seach for unique primers of a specified length.
- repeats: Filter out some simple repeats.
- search: Filters out primers for which the GC-count and/or
temperature is not acceptable and makes primer pairs.
- dcall: Convert binary files back to ASCII (for debugging).
- getinfo: Extract information from a binary data file.
- setinfo: Manipulate the information field of a binary data
file.
- statistics: Count how many factors are unique, present once,
twice, thrice or four times or more.
An online version of the search program is also
available and here is the source for those who
want to run this program on their own webserver.
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