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For each single-gene dataset, sequences were aligned using mafft v7.12751 and then manually adjusted in 4SALE52.
Sequences were aligned and manually adjusted in MEGA 5.2 for each genus.
The result obtained then is shown in Fig. 14, the threshold value Th was manually adjusted in order to get the best discrimination of defective samples.
The predicted model of transmembrane domain and crystal structure of I-II linker (5TJA) were merged, docked into the two cryo-EM maps with higher resolutions (5.8 and 5.4 Å) from mTRPML1 amphipols and mTRPML1 nanodiscs sample respectively in Chimera, and manually adjusted in Coot (Emsley et al., 2010) to acquire the atom models of state 1 from mTRPML1 amphipols and mTRPML1 nanodiscs sample.
These models were manually adjusted in order to optimize the geometry of certain regions.
Alignments were created with CLUSTALW [36] and manually adjusted in MacClade v4.08 [37].
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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.
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).
Note that we have manually adjusted α u in the bisection method and the step-size in the primal dual algorithm in order to achieve the best possible performance at the worst channel condition, that is, when the channel coherence time is the smallest one, i.e., T c 1. Figure 7 Normalized MSE of the power allocation versus SNR in a time-varying channel.
ICM said all the polls were conducted using standard telephone methodology, although it had not "manually adjusted the data in the way we would have for a national poll".
Alignments were subsequently manually adjusted and annotated in BioEdit 7.0.9 where necessary.
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