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Intervention: The women sat in a standardized sitting position and radiographs were taken in a lateral position with fluoroscopic control for alignment.
Samples were subjected to the alignment procedure during deposition on the coverslip (SI-3) except for the data described in Figure S10e (serving as a control for alignment).
The expression data for EST and full-length cDNA (FL-cDNA) of zebrafish were downloaded from the UCSC (http://hgdownload.cse.ucsc.edu/downloads.html) [ 99]. EST and FL-cDNA data processing, such as genomic mapping, quality control for alignment, and EST or FL-cDNA to zebrafish gene mapping followed [ 77], which imposed a stringent quality control to retain high-quality mappings.
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Recent studies have noted that single-alignment phylogenetic footprinting approaches often produce inaccurate or inconsistent results depending on the alignment method used, and have called for new techniques capable of controlling for alignment error and uncertainty [ 1, 8- 11].
However, for users who have identified specific genomic regions to study in detail, the benefit of controlling for alignment error and uncertainty by using BigFoot may justify the additional computational time needed for the analysis.
The programs BioEdit (ClustalW) and MUSCLE v.3.6 were used for sequence alignment, followed by a control for ambiguous alignment positions using ALISCORE v.0.2 under default settings [ 46].
As control for the alignment for each αCNS, we used a perl script to generate 10,000 "scrambled" random sequences, each representing a "random" permutation of the nucleotides that make up each CNS.
1j1m_A, which had been solved at very high resolution (1.5 Ǻ), was included as a control for the alignments with the target structure, ricin (1br6_A) (Fig. 4).
Clinical advantages include high patient acceptance, access for soft tissue care, and secure control of alignment and rotation.
Sequences were edited in Sequencher 4.8 (Genecodes Corp., Ann Arbor, MI, USA) and translated into amino acid sequences for alignment control and screening for internal stop codons or other anomalies in MacClade [31].
To control for sequence verse structure alignment, the 5' and 3'-flanking sequences are aligned using ClustalW or Mxscarna [ 47].
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