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The resulting protein alignment was reviewed and finalized using the multiple alignment sequence editor MASE.
In this study, size bias correction was applied to all entropy calculations, so that alignment sequence counts could be ignored in comparisons.
For each pairwise alignment, sequence alignment methods calculate the E-Value, i.e. the number of different alignments that are expected to occur in a database search by chance, with scores equivalent to or better than the score of that specific alignment.
BTT performed the sequence alignment, sequence analysis, and tree-drawing.
A proper alignment sequence for these paddles is a key to achieve correct functionality.
The signals include straightforward sequence alignment, sequence profile, threading, secondary structure, and exposed surface.
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The local alignment sequence-based kernels fail to precisely rebuild this structure but retain some substructures.
These alignment sequences to obtain the full-length sequences were extended from RNA-seq contig sequences.
For this alignment, sequences corresponding to the chemokine domain (Pfam PF00048 [ 63]) were extracted.
Alignment sequences are available as supporting information (see Additional files 6, 7, 8 and 9).
In the final alignment, sequences were 25% identical and ∼60% similar.
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