This was achieved using a profile based protocol that recognized differences in specificity determining residues between putative families [77].
A first HMMer search [ 24] was performed with default cut-off values of 10 using a profile based on the reference holozyme sequence set as provided by MEROPS.
Using a profile based on viewing Dr Lee's publications (top panel), MiSearch ranks two of Dr Lee's publications and a third recent and highly relevant publication at the highest relevance in a PubMed search for 'CSF1R'CSF1R
Furthermore, although we used a profile based drug discovery software, chooseLD (Insilico Science Co., Tokyo, Japan) [ 43], for in silico drug screening, it required the tertiary structure of the target protein and multiple ligand compounds whose binding structure to the protein were known.
The performance of this approach, as evaluated by cross-validation, seemed to be poor: only 4 out of 9 local recurrences and 50 of the 72 non-local recurrences could be predicted accurately in the training set at this threshold (using a profile based on 684 genes).
Second, PROFILESEARCH was used with a profile based on a multiple alignment of the Saccharomyces sequences (Fig. 6, sequences shown in lighter gray) obtained by CLUSTALW to search SWISSPROT/TREMBL (approximately 1 million protein sequences as of March 2003).
Since RSMO is a reference ontology, we modeled it using a UML profile based on UFO.
SPADA was run with an e-value of 0.1 on all available plant genomes (Table 1) using an HMM profile based on the multiple sequence alignment of group 567 from Graham et al. (2004).
Nevertheless, we have used a very sensitive HMM-HMM comparison method for annotating human domains but searched for the node of origin of those domains using a sequence-profile based method.
The structures of proteins encoded by selected genotype-specific DNA methylation associated genes were predicted successfully using two profile based methods, FAMS and Phyre2.
