Various algorithms can then be used to scan a set of sequence with this PWM to identify likely binding sites.
In order to check this hypothesis, the transferred PFM for HSF4 is used to scan a set of co-expressed heat shock genes from A. thaliana for significantly enriched transcription factor binding sites (TFBSs).
To demonstrate potential application of our method, we scanned a set of human proteins and predicted putative phosphorylation sites for Cyclin-dependent kinases, Casein kinase 2, Glycogen synthase kinase 3, Mitogen-activated protein kinases, protein kinase A, and protein kinase C families (avaiable at http://cmbi.bjmu.edu.cn/huphospho).
The druggability of the top 18-ranked proteins was assessed by using them as queries to scan a set of 305 protein drug complex structures.
It scans a set of DNA sequences for over-represented position frequency matrices (PFMs), clusters these and then estimates significance using the false discovery rate [ 42].
Visually, it is possible to scan a set of embryonic expressions and arrange them into a progression of gene expression, which informs us about the change and direction of spatial expression over time.
The conserved domain information for the transcriptome was obtained through the Pfam database [ 45] using RPS-BLAST, which scans a set of pre-calculated position-specific scoring matrices with a protein query.
We manually constructed new HMMs based on the six largest subfamilies and tested their specificity by scanning a benchmark set of all proteins that have been annotated as a member of one of the TRP subfamilies in Swiss-Prot (see Materials and Methods for details).
After 4 rounds of backcrosses with CJ06, the BC4F1 and BC4F2 generations were scanned with a set of 71 SSR markers, which were uniformly distributed on a previous linkage map (Additional file 1: Table S4).
POSSUM scanned though a set of symbols on an illuminated display.
