Genome-wide comparative analysis of annotated protein sequences in plant.

First of all, You can select any annotation groups in this database by key word search, annotation ID, Pfam domain, and blast simlarity search.Then, you can go into a window of SALAD data. All of SALAD data presented in a window were created for each annotation group. In the diagram, a colored motif indicates the position of a consensus sequence pattern that occurs repeatedly in the selected annotation group. Therefore, discovered motifs may be distinct in different annotation groups if you see the same annoation in the groups. Thus, to avoid misunderstanding and get new more insights, we recommend you to refer to several annotation groups about the same target annotation of yours. In addition, SALAD database has function of intaractive SALAD analysis, please try it.

Our algorithm for clustring of annotation is based on presence and similarity scores of the extracted conserved motifs. For that reason we can't disscuss about phylogenetic evolution well. When you are intersted in phylogenetic relatiobships among the target annotations, please use a SALAD database function of making NJ phylogonetic trees based on alignment information from sequences of conserved motifs. You can select multiple motifs together to make the trees at once.

Empirically defined parameters were used for calculating the similarity scores, and any disturbed clusterings have been reported rarely.