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SALAD database: a motif-based database of protein annotations for plant comparative genomics
Motohiro Mihara1, Takeshi Itoh, Takeshi Izawa
1Plant Genomics Research Unit and Bioinformatics Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan.
Nucleic Acids Research
|October 27, 2009
Summary
The SALAD database integrates plant proteome data, identifying conserved protein motifs to reveal evolutionary relationships and functional similarities. This tool aids biological analysis by comparing protein sequences and their evolutionary histories.
Area of Science:
- Comparative genomics
- Bioinformatics
- Molecular evolution
Background:
- Proteins contain motifs with diverse evolutionary origins, influencing biochemical properties and biological functions.
- Understanding protein motif evolution is crucial for deciphering protein function and relationships.
Purpose of the Study:
- To develop a comprehensive comparative genomics database (SALAD) for analyzing evolutionarily conserved protein motifs.
- To provide tools for visualizing motif patterns, phylogenetic relationships, and functional similarities across species.
Main Methods:
- Extracted conserved motifs using MEME software from 209,529 protein groups across 10 diverse species.
- Utilized BLASTP for protein sequence annotation and pairwise scoring for motif pattern similarity clustering.
- Constructed phylogenetic trees and generated graphical viewers for motif patterns, dendrograms, and Pfam domains.
Main Results:
- The SALAD database offers a user-friendly interface for visualizing motif patterns, bootstrapped dendrograms, and phylogenetic trees.
- Includes tools for comparing amino acid and nucleotide sequences, logo diagrams, and Pfam domain patterns.
- Developed 'SALAD on ARRAYs' for integrating microarray data with paralogous gene analysis.
Conclusions:
- The SALAD database is a powerful resource for comparative protein sequence analysis.
- Facilitates the identification of evolutionary relationships and functional insights derived from conserved protein motifs.
- Supports biological research by providing a robust platform for exploring proteome data.
