The values of NA and NC indicate the scale of the alignment.
Recently, we introduced a new class of RGCs designated RGC_CAMs (after conserved amino acids-multiple substitutions), which are inferred from genome-scale analysis of alignments of orthologous proteins and underlying nucleotide sequence alignments (Rogozin et al. 2007a, 2007b).
Together with the development of large scale structural alignment tools [ 15], this allows to conduct a comprehensive comparison of protein structures among GIs.
The AST is an over 250-km-long, 60-km-wide subglacial trough, elongated in the NNW SSE direction adjacent to the westernmost flank of the Wilkes Subglacial Basin, and is parallel to regional scale alignments of magnetic and gravimetric anomalies.
Procrustes superimposition was used to remove the effects of alignment, rotation or scale.
Exact scaling properties are predicted, including explicit Leslie alignment angle and degree-of-alignment (birefringence) formulas, as well as normal and shear stresses, in terms of molecular parameters and normalized shear rate for dilute nematic polymers.
We calculated the FF with different degrees of alignment to fine-scale behavior.
The raw 75 bp Solexa reads of the gsNd database were analyzed by the mapping algorithms, Efficient Large scale Alignment of Nucleotide Databases (ELAND), which is built in with the Solexa sequence analysis pipeline of the Illumina sequencer [ 24].
For improving the search accuracy, we used our recent (large scale) alignment of σ70 promoter elements in E. Coli [ 19].
The process can be viewed as a combination of signal space and signal scale interference alignment.
