Annotation of Proteins from LOD for a Viewer of Multiple Protein Sequence Alignment

Recent progress in sequencing technology has caused so-called data flood of nucleotide and amino acid sequences. Such enormous amount of data can increase the reliability in prediction of structures and functions of proteins based on a multiple alignment. At the same time, however, it has become difficult to analyze a multiple alignment with the user-interactive manner due to the volume of sequences constituting the alignment. Therefore, we have worked on developing an alignment viewer that is referred to as ASHViewer. In this study, we focused on the annotation for a large number of proteins which is essential for the comparative study with alignment. To obtain various types of annotation for a large number of proteins all at once, we employ a method that uses federated query search along a path of class-class relationships. To clarify the effectiveness and problems using the method for alignment viewer, we implemented a prototype system of federated query search called PSurfer.