NAR Molecular Biology Database Collection entry number 1296
Xu, Ying; Mao, Xizeng; Ma, Qin; Zhou, Chuan,; Chen, Xin''; Zhang, Hanyuan; Yang, Jincai; Mao, Fenglou; Lai, Wei
The SALAD database is a unique plant comparative genomics database of similarity clustering, based on distribution patterns of evolutionarily conserved motifs. Comparison of distribution patterns of motifs among related proteins enables us to infer biological functions of the proteins of interest and to get hints for designs of next experiments since proteins with similar motifs may have similar biochemical properties and thus related biological functions. In the latest version (version 3), the motifs were extracted by MEME software from 209,529 'high-similarity' protein groups selected from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting dendrogram for each protein group. Phylogenetic trees based on aligned motifs and amino acid (nucleotide) sequence comparison by logos are also available. A novel viewer termed "SALAD on ARRAYs" enables users to compare arbitrary microarray data sets of paralogous genes in the SALAD clustering dendrogram.
We thank the members of LM-Microarray of Rice Pollen Project for providing microarray data. We also thank IRGSP and RAP members for rice genome sequencing and annotation, the JGI, and other consortia for providing genome data sets. This work was supported by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (Agrobiological Genomics project, Genomics for Agricultural Innovation project).
Category: Plant databases
Subcategory: General plant databases
Go to the abstract in the NAR 2014 Database Issue.
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