The phrase "alignment the background" is not correct in written English.
It seems to be missing a preposition or verb to make sense in context.
Example: "We need to ensure the alignment of the background in the design."
Alternatives: "align the background" or "background alignment."
MN collected the data and divided the data into partitions, planned the experimental set-up, did the manual training in ILink and the manual categorisation in IViev, analysed the data and wrote the article except for the sections 'Word alignment' in the 'Background' and 'Alignment tools' and 'Ranking and filtering candidate term pairs' in the 'Methods'.
MM configured, ran and calculated the results from the experiments in ITools, substantially contributed in the design of the study, wrote the sections 'Word alignment' in the 'Background' and 'Alignment tools' and 'Ranking and filtering candidate term pairs' in the 'Methods' and substantially contributed to drafting and revising the remaining parts of the manuscript.
The logos produced by Spial appear similar to those produced by the program Two Sample Logo (Vacic et al., 2006), which treats one alignment as the background and then computes whether there are residues that are enriched or depleted in the other alignment.
Followed by filtering out the pairs with TM-score [ 80] lower than 0.65 which indicates that the two proteins have no obvious biological relevance [ 81], we calculate the log-odds ratio between the pair frequencies in the remaining structure alignments and the background frequencies, with respect to the relative solvent accessibility in 1% unit.
Empirical p-values for the SigB HMM alignments were determined by comparing the alignment score to the background scores using a Perl script and R-2.13.0 R-2.13.0
We compared two sets of models, the first set focused on comparing changes in ω (= dN/ dS) along the branches of the tree, and the second set of models focused on comparing changes in ω along the different sites in the alignment between background and foreground sets of branches.
E-values for the traditional structural alignment are derived by using the background information, i.e., the distribution of alignment scores for random proteins that are structurally dissimilar to the query protein.
Thus, the sequence similarity between the two species is in the 'twilight zone' of detection by alignment, i.e., orthologous open reading frames have alignment scores just marginally above the background of unrelated sequences.
Thus, even when the G/S value exceeds 80percentt of the length of the alignment (orange color background), as much as 70percentt of the branches are reconstructed accurately by MP (Panel I), and 90% by the Bayesian method (Panel G), when the gaps are treated as binary characters (BC), and the insertion-deletion ratio is 1 1.
The 'All Positions' column gives the percentage of non-conservative pairs relative to each property partition over all alignment positions and serves as the background reference point for each partition and the significance calculation.
