Sentence examples for alignment models were from inspiring English sources
The upper bound (lamellae aligned in parallel with respect to the permeation direction) and lower bound (series lamellar alignment) models were calculated and compared to a limited amount of corresponding experimental data on oriented specimens.
Our alignment model is expressed as a pairwise HMM transducer [ 29, 30], a conditionally normalized HMM representing the evolution of an ancestral sequence into a descendent sequence, and is similar to the transducer model in [ 20].
Briefly, based on each individual alignment, initial models were generated by copying atomic coordinates for the main chain (excluding any insertions/loops) and for the side chains of residues that were identical in the target and template proteins.
Based on ClustalW alignments, three-dimensional models were generated by comparative protein modeling with MODELLER program [ 70] as implemented in Discovery Studio 3.5 (Accelrys Inc .. Twenty models, optimized by a short simulated annealing refinement protocol available in MODELLER, were generated for each globin chain.
CEPD antenna alignment mismatch models are derived from dedicated measurements followed by a CEPD selection procedure and multi-rate filter processing.
Local alignment models (fs) were used.
Based on different alignment rules, several computational models were established with their statistical results compared.
Based on docking and database alignment rules, two computational models were established to compare their statistical results.
The multiple sequence alignment and the 3D models were displayed using ESPript [ 68] and PyMOL [ 69], respectively.
For each target-template alignment, ten different target models were built, and their quality measures were assessed using the GA341 [ 19, 20] and QMEAN methods [ 21].
Subsequently, HMM models for SCRiPs were iteratively built by using the first discovered SCRiP as an initial model and appending newly discovered proteins to form multiple sequence alignments upon which the models were built as described above.
