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The alignment of each template residue in the structure-to-structure alignment produced by TM-align was compared with the alignment of the same residue produced by one of the methods.
– indicates alignment of the same sequence.
This allowed the precise alignment of the same imaging volume over a period of 6 weeks.
The multiple sequence alignment of the same gene requires Jalview java applet to display.
The alignment of the same dataset was repeated with two well-known long reads alignment tools: BWA-MEM and BLASR.
This allowed a precise alignment of the same imaging volume over a period of up to 15 months.
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In other words between the range of St.1000 St.5400 of Fig. 5, the SSD adequacy investigation of 23 compound alignments of the same horizontal (R = 1000 m) and vertical (K = 200 m) geometry is delivered.
Different alignments of the same protein family give different results demonstrating that covariation depends on the quality of the sequence alignment.
Up to 3 mismatches were allowed and multiple alignments of the same oligonucleotide sequence were discarded as they indicated ambiguous positions due to problems with the genome assembly or with the oligonucleotide design.
This observation is supported by Wong et al. [20] who found that alignments of the same sequence dataset by different methods lead to different conclusions in comparative genomics studies.
As a control, multiple sequence alignment blocks were shuffled using a randomization algorithm that takes care not to introduce randomization artifacts and produces random alignments of the same length, base composition, overall conservation, local conservation pattern, and gap pattern as the input alignment [44].
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Justyna Jupowicz-Kozak
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