Universität Bielefeld
- Technische Fakultät
- AG Praktische
Informatik
Searching for regulation motifs
in the
human heparin cofactor II gene
Introduction
The aim of this
study-project was to search for possible motifs in the human heparin
cofactor II gene that permit the regulation of the heparin cofactor II
synthesis. For this reason, sequences and structures of these genes, which
were extracted out of human, rat, mouse and rabbit were compared to
each other.
The available methods in bioinformatics allow to find possible sequence
motifs, which can be useful starting points for expirmental analysis.
Methods
The following methods have been used:
- Multiple sequence alignment:
Shared signals are exptected to lie in conserved regions of the
sequences. The method of choice to specify these conserved regions
is to compute a multiple sequence alignment. For this purpose
the program DCA
was used.
- Secondary structure predictions with thermodynamic information:
The long, unbranched and single-stranded chains of RNA
molecules tend to fold to double-stranded forms. The secondary
structure of a RNA molecule can be computed by using the free
thermodynamic energy of the molecule. For this purpose the
program MFOLD was used.
- Combination of both phylogenetic approach and thermodynamic approach:
The Construct-package takes
advantage of the combination of either approach. The optimal
secondary structures were computed for each sequence. In the second
step the gap positions that were taken from the multiple
sequence alignment were included forming a consensus
structure.
Results
The results show several structures that might be good starting points
for further investigations, though they suffer in the small number of
available information, above all the small number of sequences.
This study-project
has been finished now. It has taken approximately five months time part-time.
If you want more information, please contact the authors:
Hermann Ragg (hr@zellkult.techfak.uni-bielefeld.de)
Robert Giegerich (robert@techfak.uni-bielefeld.de)
Ole Bents (obents@techfak.uni-bielefeld.de)
August 1997