ρ (A r) reflects the alignment quality of the rth column in A, giving high scores for aligning nucleotides of the same type and penalizing alignment of nucleotides of different types or aligning nucleotides against gaps.
Searching on atom types favors alignments that superimpose atoms of the same type.
Their clustalW alignment revealed the same type of pattern as their bulk counterparts, with less complexity and, hence, more homogeneity.
We use the SIM procedure [ 27] to compute the sum of the k-best alignments (k = 2,..., 5) within the same type of Markov-chain Monte Caslo sinulathen as in the previous sections.
The position is of the same type.
More interestingly, when we marked the HLA-restricted epitopes on the alignment sequences of the proteins, we found that the epitopes restricted by the same type of HLA allele are located at the same domains of the proteins.
In assembling his own group, he found "the stars really have to be in alignment," he said, "to meet nine other guys who are into the same type of music and willing to do what needs to be done".
The alignment to the Abp1-mCherry is valid, because the systematic shift is common for the same type of fluorescent protein.
Two NCIVs (each from one interface) are matched in the alignment if they represent the same type of non-covalent interactions, and have similar distances and relative orientations to the other matched NCIVs within the respective interfaces.
Due to the low number of protein types (see Table 4), D1 and D2 might contain alignments of the same protein types.
To determine how the G93A mutation may alter structure in the 90 93 loop, we performed the same type of structure alignments for the available structures of the G93A mutant (16 subunits from 3 distinct crystal structures; Figure 2b).
