Sentence examples for normalized alignment from inspiring English sources
The structural diversity (S-div) defined as the RMSD divided by the normalized alignment size (see [41] and Formula 2) is conceptionally the simplest one and the Q-score [43] is a measure with a clearly defined range (0 to 1); these two measures also showed high performances in our experiments and were thus extensively used in this study.
Normalized alignment score (NAS) measures similarities between a protein sequence and the querying sequence.
The bitscore is a normalized alignment score taking into account the underlying HMM scoring scheme, which is the same (in our case) for both models.
To determine λ and μ, normalized alignment scores from the random alignments described above were fitted to the cumulative density function, F x)= exp(− exp(−λ(x−μ))).
The homologous sequences are then sorted in descending order by their normalized alignment score (NAS), which is the alignment score divided by that of the query sequence itself.
After the completion of all the hmmpfam searches against the training and test set of genomes, using both the Pfam and FPfam HMMs, the hmmer normalized alignment scores (known as bitscores) were extracted.
Observed p53-occupied sites in the PC12 genome were visualized by plotting normalized tag alignment locations relative to a hypothetical gene size of 100 kb.
The pairwise similarity of two condition-specific motif sets is expressed as the average of normalized best alignment scores (see above). Figure 4B indicates that condition-specific motif sets from different prediction pipelines show high similarities of ≥ 80% on average.
We define Impact as the normalized difference between Alignment and Alignment∗.
Then the SVR model is used to predict the PFM similarity of the query TF to all TFs with known PFM in the same superclass, whenever their DNA-binding domain similarity exceeds 0.3 (normalized Needleman-Wunsch alignment score with BLOSUM62).
InParanoid which uses BLAST to compute sequence similarity does significantly worst that BBH using normalized Smith-Waterman alignment scores.
