It relies on the subroutines Align, which returns the best alignment between two series based on a given set of genes, and ScoreGene, which returns the score of two series when aligned using a given alignment and a specified gene.
The predicted secondary structures were aligned according to the protein alignment and a consensus prediction was generated using the Jalview software [ 63].
PRALINE provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided alignment and a reliability measure for aligned individual residue positions.
This extended homeodomain was extracted for each of the eight D. melanogaster Hox-proteins, aligned in AlnEdit using Muscle (see Appendix S3 for the extended homoedomain alignment) and a global HMM was derived from this alignment using HMMer.
Correctness was checked by alignment, and a contig is considered as correct if it can be aligned to a reference with 95% similarity by BLAT (Kent, 2002).
Alignment Plans Officials plod on trying to devise an alignment and a schedule format for next season.
But if this exquisite balance is disturbed, usually by an injury, the loading mechanisms shift, the moving parts of the knee are no longer in their accustomed alignment and a "degenerative pathway" seems to open.
A decent eight-inch Schmidt-Cassegrain telescope with a computerised alt-azimuth mount, GPS alignment and a proper tripod will cost around $3,000 new, and perhaps half that second-hand.
However, it uses time-consuming multiple sequence alignment and a low-accuracy greedy clustering algorithm.
As the solvent evaporated, the capillary force pulls CNT closer together, resulting in a CNT paper with a high degree of alignment and a high packing density.
