The parameter's default setting was used for the MetaGenomeThreader, where only the minimum length of the amino acid sequences, which should appear in the result output, was set to 30 amino acids. Opposing the long DNA sequences the extended-modus was switched off (cp. test data: long DNA sequences). Based on the changed DNA sequences of the identified PCS's, and the changed protein sequences compared to the target protein sequences, an alignment of the protein sequence of the identified PCS's and the target protein sequences is not very useful. An alignment of the identified PCS's protein sequence with a protein database is being executed to determine whether the target protein sequences can be detected.
To evaluate the result, the identified PCS's were ordered in clusters as an alignment to the related target sequence. The bottom amino acid sequence (lowercase) is the protein sequence of the target protein (cp. Tab. 1.1). The identified PCS's are written in uppercase letters.