SALAD

SALAD analyzes evolutionarily conserved motifs in proteome datasets from plants and related species to support comparative genomics and evolutionary analyses.

Key Features:

• Comprehensive dataset: Protein-sequence annotation groups compiled from 10 species (rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, three algae, and yeast) comprising 209,529 protein sequences selected using BLASTP.
• Motif extraction: Evolutionarily conserved motifs are identified from protein sequences using the MEME software.
• Similarity clustering: Pairwise scoring of motif patterns is used to perform similarity clustering for each protein group.
• Phylogenetic analyses: Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees, bootstrapped dendrograms, logo comparison diagrams for clades, and Pfam-domain pattern diagrams are provided for motif-combination alignment and interpretation.
• Microarray data integration: Microarray expression datasets of paralogous genes are linked to protein-group dendrograms to relate motif-based clustering with expression patterns.

Scientific Applications:

• Comparative genomics: Cross-species motif comparisons support identification of conserved sequence features across plant and related genomes.
• Evolutionary biology: Motif patterns and bootstrapped dendrograms enable inference of evolutionary relationships and histories within protein families.
• Functional inference: Conserved motifs correlated with biochemical properties and Pfam domains facilitate hypotheses about protein function.
• Target identification: Conserved sequence features across species can guide selection of candidate targets for genetic engineering or drug development.
• Integrative analysis: Linking phylogenetic trees with microarray expression of paralogs aids interpretation of gene-family evolution and expression divergence.

Methodology:

Protein sequences are selected by BLASTP, motifs are extracted with MEME, motif patterns are pairwise scored and clustered, and phylogenetic trees and bootstrapped dendrograms are generated alongside logo comparisons and Pfam-domain pattern diagrams.