SALAD -- Surveyed contained motif ALignment diagram and the Associating Dendrogram
What you can do:
Perform systematic comparison of proteome data among species.
Highlights:
- SALAD is a comparative genomics database from plant-genome-based proteome data sets.
- Evolutionarily conserved motifs were extracted by MEME software from 209,529 protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast.
- Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences.
- The SALAD database provides a graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group.
- Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available.
- 'SALAD on ARRAYs' is a viewer to view arbitrary microarray data sets of paralogous genes linked to the same dendrogram in a window.
Keywords:
- protein motif
- comparative genomics
- comparative proteomics
Literature & Tutorials:
This record last updated: 04-28-2010