GCG Package

Comparisons are with the pghD12-l sequence employing the Gap program of the GCG package using a gap weight of 3.0 and length of 0.1. 

Accelrys provides data management and sequence analysis tools through the DS SeqStore and GCG Wisconsin Package products, running on UNIX systems. DS Gene provides PC access for visualization and analysis capabilities within the Discovery Studio product family. 

We infer that it is unlikely that the thermophile terminators resemble bacterial rho-independent terminators. Moreover, this view is reinforced by examining the sequences for the bacterial terminators using a program in the GCG-software package from the University of Wisconsin. This is based on the observations of Brendel and Trifonov [125] that in addition to the inverted repeat preceding a polythymidine sequence many bacterial terminators share sequence features located both upstream and downstream from the termination site. Only one of the termination sites shown in Table 5 is predicted by this program. 

The alignments are imported into the GCG 11.0 software package, and corrected manually for alignment error in the Editor mode (see Note 6). 

GCG Wisconsin Package http //www.accelrys.com/products/gcg wisconsin package/index.html MEME http //meme.sdsc.edu/meme/website/meme.html... 

Womble, D. D. 2000. GCG The Wisconsin Package of sequence analysis programs. Methods Mol Biol 132 3-22. 

Program Manual, GCG Sequence Analysis Software Package. Genetics Computer Group, Inc., Madison, Wl. 

Calculated based on comparison tables using the GCG program package. Measured by thermal unfolding at pH 7 using CD spectroscopy. 

In order to optimize codon usage in a synthetic gene, the frequency of codon usage must be included with the run (Fig. 3). Codon frequency is determined using the method of Nakamura et al. (8). The codon frequency table also directs the reverse translation of amino acids to codons. The format is that of the GCG Wisconsin Package. 

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