Sentence examples for block in the alignment from inspiring English sources
(ii) Delete the worst-fitting aligned pair that appears at the end of a 'matched block' in the alignment, and force the deleted pair of residues to be unaligned.
The score of a syntenic global alignment is the sum of the values of each match, mismatch, gap and unconserved block in the alignment.
Gblocks was used to extract the conserved blocks in the alignment.
The annotation file provides detailed information including chromosome localization, transcription direction, blockCount (number of blocks in the alignment) and blockSizes (comma-separated list of sizes of each block).
Most of the separated blocks in the alignment are associated with integrases and/or IS elements on at least one of their borders.
For each block, b in the alignment containing nb sequences and mb columns, the ith column of the block is assigned a score Cbi = 1 if all the residues in the column are aligned correctly, otherwise Cbi = 0.
For each block in the reference alignment, the maximum score obtained by any of the programs was selected and these maximal block scores were then averaged over the whole alignment.
A repeat block is considered correct, if exactly the same region in X and the same region in Y are also forming a repeat block in the true alignment.
Given these definitions, the score of a syntenic global alignment (mathcal A ) is the sum of the values of each match, mismatch, gap and unconserved block in this alignment.
To investigate the ability of the MSA programs to identify context-specific or locally conserved motifs, we typified each individual block in the reference alignments using a number of different features: block length, sequence similarity in the block, the frequency with which the block is observed in thealignment, and the percentage of the block found in a natively disordered region.
This fragment and the corresponding part in the other taxa were kept as separate blocks in the final alignment, with the characters of one block coded as missing (see 'Yponomeuta nexus file', Text S1 in the Supplementary Material).
