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We set a maximum alignment score of 125.
This strategy avoids reference alignment bias of other tools (e.g., samtools rmdup) that select reads with maximum alignment score.
Reads with a minimum of 80%% of maximum alignment score were analysed further, after which the actual nucleotides at the potential methylation sites were summarised.
The identity in the window was given the maximum alignment score by ClustalW [ 43] in each position of the mouse RP genes.
First, the maximum alignment score from all the pair-wise DP sequence alignments are bounded by b, where b is the max pair-wise score between any two residue symbols.
In the case of the Needleman-Wunsch's algorithm, cell c n, n holds this value; and in the case of the Smith-Waterman's algorithm, cell c i, j with the maximum alignment score is the end point.
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During the process of a broad search, node pairs with maximum alignment scores are selected and aligned.
Alignment algorithms find optimum alignments and maximum alignment scores S of two or more sequences for a given scoring system.
Maximum alignment scores are identified as the primary read; if multiple scores exist, the read is marked as ambiguous and not utilized.
Based on the alignments, a maximum likelihood tree was constructed.
The maximum local alignment score refers to the maximum score in H function.
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