Form the new consensus sequence from this multiple alignment of the two aligned sequences by finding the nearest frequency column cluster in each position.
Following building the profile alignment for group I and group II separately, the two aligned profiles were merged using profile alignment option from ClustalX.
To measure correctness, we compute Smod, the ratio of the number of correctly aligned positions to the number of aligned columns in the evaluated alignment where at least one of each two aligned columns is present in the reference alignment.
As the 454 reads were shorter and the E-value of an alignment is directly proportional to the product of the lengths of the two aligned parts, we used for 454 read alignments an E-value cutoff of 10-7.
Distances between motifs were defined as the absolute deviation between the nucleotide frequencies of two aligned positions in the best local alignment.
Analogous to conventional sequence alignment without weights, the similarity between two aligned sequences can only be measured with sequence identity.
An estimate of the expectation value of an alignment provides a good assessment for whether the two aligned proteins are homologous [ 17].
The higher the score is for a pairwise alignment, the higher the degree of conservation is between the two aligned sequences.
The property includes two aligned rectangular structures separated by a small patio.
For the biomimetic scaffold, the scaffold was oriented with the two aligned longitudinal layers defining parallel.
The non-dimensionalization of motion equations for the crossflow of a power-law fluid between two aligned cylinders was performed using this philosophy.
