SalMotifDB is a genome wide map of putative transcription factor binding sites (TFBSs) for salmonids and related fish genomes. The database contains predicted binding sites identified in the upstream promoter regions (-1000/+200 base pairs) from transcription start site (TSS) in salmonids and several relatrd fish genomes. The database was developed by scanning the promoter sequences using over 12,000 position specific scoring matrices (PSSMs) collected from different public and commercial motif databases.
The motifs source databases store redundant classes of TF binding profiles as PSSMs. To filter out the redundant information in our motif source database, we clustered all PSSMs using the matrix-clustering tool in RSAT. First, we clustered TF binding profiles within each database. Then, we clustered the results from each collection databases for further classification.
Segment plot of shared motifs between Atlantic salmon and each species in the orthologous groups inferred from an alignment of protein sequences of Oncorhynchus kisutch, Oncorhynchus mykiss, Salmo salar, Esox lucius, Gasterosteus aculeatus , Oryzias latipes , Danio rerio , Homo sapiens and Mus musculus