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A peak towards index value of 1 implies high similarity between the maps, compared with linearly increase of random distribution of alignment indexes (in red line).
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.
Overall, the distribution of alignment bit score along the BAC clone closely followed hybridization success.
Fig. 2 shows typical examples for the distribution of alignment sites with low and high reliability scores q.
The distribution of alignment depth and divergence in this training set allows empirical thresholds to be determined.
Default parameters were used and 1000 reshuffled sequences were used to generate the random distribution of alignment scores.
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Any individual alignment could indicate a direction by chance, but he planned to show that together the distribution of alignments was non-random, showing that there was an astronomical intent to the orientation of at least some of the alignments.
"Statistical alignment" [ 12] methods provide a framework for performing comparative genomic analyses while considering a probability-weighted distribution of alignments.
Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction.
The joint posterior distribution of alignments, trees and evolutionary parameters forms a high dimensional and complex distribution from which efficient direct sampling is most likely impossible.
(DOCX 15 kb) Additional file 6: Distribution of alignments of the transcripts of the de novo transcriptome of S. frugiperda by species obtained via BLAST.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com