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Because of length variations between the sequences, we modified the procedure of Ding et al. [ 48] and defined two sequences as paralogs if the aligned regions were over 70% of the shorter sequences.
A phylogenetic analysis revealed a close relationship between the sequences we obtained and a TBEV sequence from Mecklenburg-East Pomerania published in 1992 and pointed to the reemergence of a natural focus of TBEV after years of low activity.
The close relationship between the sequences we found and the single published sequence from Usedom from the year 1992 (IZ-11/1992) may indicate that the TBEV-foci in Mecklenburg-West Pomerania persisted over the years at low levels of activity.
Any evolutionary study of a large set of diverse organisms is likely to reveal a complex history, so to aid further analysis of the relationships between the sequences we classified them into six types using key sequence and structural signatures that define apparently monophyletic groups (such features are also known as synapomorphies).
Overall, we found no obvious similarity between the sequences we obtained for collagen-specific expansions (including that of the BV1-BJ2.6+ cells homing to the synovia) and those that were described in the synovia of a large collection of RA patients [ 21].
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To improve the resolution of the phylogenetic relationships between these sequences, we carried out an analysis of the sequences composing this cluster and close relatives using several more distantly related sequences as outgroup.
To further asses the phylogenetic relationship between the USP/RXR sequences we removed all the HNF4 and EcR sequences and performed a new phylogenetic inference with only these sequences.
To determine whether there was a difference between the two sequences we first fitted a linear function to the main sequence of session one and then used this model to predict saccade amplitudes using the peak velocity data from session five saccades.
LCRs from the four other primate species were found and compared with find orthologs based on location within the protein as well as identity between the sequences, and we identified 5,584 LCRs (in 2,425 genes) shared by all five species (table 1).
To assess the age of the divergence between sequences, we estimated the level of synonymous substitutions (Ks) between the Arabidopsis thaliana HAM1 and HAM2 genes.
To compare the similarity between symbolic sequences, we plotted the rank number of each n-tuple sequence in the first sequence against that of the second sequence (Figure 1B).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com