We present the latest result of our research:
Sierra Platinum is a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. It allows to generate peaks while the user influences, which replicates are most suitable for creating them. The results show that the new method outperforms available tools and methodologies.
One important topic in Bioinformatics and Biology is studying diseases that are caused by genetic defects. For a long time it was supposed that the genome is responsible for all properties, e. g., hair and eye color, gender, and size. At the beginning of this millennium, however, a new field besides genetics appeared: epigenetics. Epigenetics studies the hertiable changes in the cell nuclei that do not stem from the genome, only. In fact, the cell type, e. g., brain cells, muscle cells, or tissue cells, is not determined by the genome. All cells contain more or less identical genomes (changes due to copying during cell replication might occur). Epigenetic features determine the cell type.
The genome can be considered as a long sequence of molecules, the so-called nucleotides. However, if the genome is unfolded as a straight line, it would not fit in a human cell. In fact, it is tightly folded inside the cell's nucleus. For this, it is wrapped around a complex of eight proteins, the so-called histones. This histone complex and the DNA wrapped around it are also called nucleosome. The proteins can be modified. One possible type of modification is called methylation, where a methylgroup is added to the protein. The proteins are very large, thus that methylations can occur at many different places at the protein.
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