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Sequences of the individual genes were aligned using CLUSTAL X [66] or MAFFT [67] and manually corrected in BIOEDIT (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
Alignments were performed separately for each gene using ClustalW [ 21] and manually corrected in SEAVIEW [ 22].
The resulting trimmed alignments were checked and manually corrected in BioEdit v7.0.5 [ 120].
The model was manually corrected in COOT [ 30] and refined in REFMAC [ 31].
The obtained segmentation using implemented snake evolution algorithm was manually corrected in the three orthogonal planes for all cases.
The initial model of the RII tetra-tandemer was built using CCP4-Buccaneer [ 16, 18] and was manually corrected in Coot [ 19].
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Later, the automatic parameters can be manually corrected [16], in order to reduce inevitable misdetections and enforce linguistic criteria.
Furthermore, we manually corrected the artifacts in four patients from GroupINNER and seven patients from GroupOUTER, and by comparing the MR-AC maps and their resulting AC-PET images, we found that our automatic correction method produced very similar results.
Alignments were then manually corrected and masked in SeaView (version 4.2.4) (Galtier et al. 1996).
However, to ensure an accurate calibration, we manually corrected the points in case of recognition failures.
ARS conducted all the software analyses, manually corrected annotation errors in the five genomes, developed the prediction schema and wrote the paper.
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