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A result image of adjusted alignment is demonstrated to show the reduced discrepancy by using the alignment measurement method.
The sequence similarity between adrb2 and drd2 in the manually adjusted alignment was 35%% in total, 41%% in the helix regions, and 57 % in the binding pocket.
After removing the PCR recombination sequences from the analysis, we again adjusted alignment of the remaining 1,336 sequences using ClustalX.
Two OR sequences of L. crocea were removed from the adjusted alignment because they were found to be the same as two other sequences after removal of the N- and C-termini.
The sequence similarity between adrb2 and drd1 in the manually adjusted alignment was 36%% in total, 43 % in the TM helix region, and 67%% in the binding pocket (the corresponding sequence similarity between drd1 and drd2 is 34, 43, and 55%%, respectively).
The adjusted alignment after manual correction was used for phylogenetic analyses by maximum likelihood (ML) and maximum parsimony (MP) methods.
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Neighbour Joining (NJ) trees were constructed in ClustalX v.1.83 using the manually adjusted alignments with the following parameters: 10000 bootstraps, 1000 seeds and correction for multiple substitutions.
The HMMs were created using HMMER3, with manually adjusted alignments of representative sequences as seed.
Insertions and deletions unique to nematodes were identified based on the adjusted alignments.
This precision task requires the exact manual positioning of the tape and a careful visual control in order to continuously adjust alignment and to check for any air bubbles fastened under the tape.
Current methods of fixation require a surgeon to visually align segments of bone and affix a metal plate using bone screws, after which little can be done to adjust alignment.
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