Prot4EST [ 48] was then used to predict open reading frames (ORFs) using the following criteria: 1) if a unigene had a significant BLAST hit with Uniprot, the ORF from the best hit was used as template for ORF prediction; 2) if the unigene had no BLAST hit, ESTScan [ 49] predicted peptides that were used to predict ORFs.
The E2s structure of the HEV (PDB: 3GGQ) was used as a template for epitope prediction (Li et al., 2009).
Instead, a crystal structure of the ChR chimera (C1C2), an engineered combination of helices I V from ChR1, without its C-terminus, and helices VI VII from ChR2, is used as a template for ChR2 structure prediction.
The structures of SiCYS-N and SiCYS-C appeared alike using those structures as templates for structural prediction.
These expression patterns of hypothetical samples representing the subclasses are used as templates for the prediction.
For instance, no server found the correct template for T0460, and confident predictions were not possible for T0465, T0466, etc.
The protein sequences of these three species were compiled and used as a reference gene set template for homology-based gene predictions for the newly assembled bird genomes.
In such cases, the template prediction for the flanking TMHs should be used to guide the loop template selection.
The development of many different TM-helix prediction algorithms and the recent upsurge of GPCR structures (for a review, please see Venkatakrishnan and coworkers 42) have prompted us to consult multiple prediction programs and alternate templates for TM-helix prediction and in homology modeling, respectively.
This may have implications in terms of using rice as a template for gene discovery and gene function prediction in the larger genome monocots.
