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Beschreibung:
Modern molecular biology research is characterized by the availability of an increasing amount of biological data which is often fuzzy due to the nature of the experimental methods used to derive it. Bioinformatics, a branch of computer science, deals with the storage, retrieval, and analysis of this data. DNA, the basic information carrier of life, is now sequenced industrially in large quantities and assembled to complete genomes. The automatic annotation of genes in these genomes, a process called computational gene structure prediction, is the scope of this thesis. This dissertation describes the computational gene structure prediction software GenomeThreader which uses homologous biological sequences (so-called cDNAs/ESTs and/or protein sequences) to predict gene structures by computing spliced alignments. GenomeThreader uses a multi-phase approach, filtering the possibly very large sequence data sets in early phases to obtain promising gene candidates which are then refined by more computationally expensive algorithms in later phases. The results of this gene structure predictions, genome annotations, can become quite large and cumbersome to process. To deal with such annotations easily and efficiently, the GenomeTools genome analysis system has been developed, which is also described in this thesis. The prediction quality of GenomeThreader was evaluated on a variety of datasets and the results show that the software performs very well on common gene structure prediction tasks. The quality of the results is comparable with the results of the best other programs and in some cases it is even better. The software is very easy to use due to its integrated nature, a feature which distinguishes it from its competitors. GenomeThreader has been adopted widely in the scientific community, it has approx. 150 users world-wide and over 30 publications cite the scientific article which describes an earlier version of the software. The open source package GenomeTools was used as a foundation for 10 published sequence ...