Sentence examples for extension alignment from inspiring English sources
On the turnpike extension alignment proposed in 1994, Route 92 was to begin at a trumpet interchange with U.S. Route 1 in South Brunswick.
We used two different approaches to alignment (direct optimization and homology-extension alignment) and tree building (parsimony and ML), to illustrate the effect of very different data treatments.
Another current challenge is the extension of reference alignments with fragmented sequences, as those coming from next-generation metagenomics, that contain relatively little information.
We tested PAGAN in the extension of real reference alignments with new protein and DNA sequences and found that it can successfully handle data of great variety in length and evolutionary divergence as well as different sizes of reference alignments.
Hmmalign has been used for the extension of reference alignments with new sequences in metagenomic analyses (Matsen et al., 2010; Stark et al., 2010) and recently Mirarab et al. (2012) developed an approach that applies hmmalign on subsets of the reference alignment.
The extension and alignment process is repeated until a final consensus set is converged upon or until the completion of a predetermined number of iterations.
Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy.
One major source for such false positives is profile corruption, usually resulting from extension of alignments over non-homologous sequence regions (Galperin and Koonin, 1998).
Sequences were aligned using Clustal × version 1.83 [ 59] with default penalties for gap opening and gap extension, and alignments were visually verified.
PAGAN and hmmalign were consistently the two most accurate methods for the extension of alignments with new DNA and protein sequences (Fig. 4).
