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The level of deformation from native geometry was measured with the FAST algorithm [31], which for each value c calculated a corresponding alignment fraction f, defined as the number of aligned residues over the total number of residues.
All DNA sequences obtained were aligned using ClustalX program [ 63] and corresponding alignment was used to analyze the relationships between families.
As expected, the fiber alignment of the gradient meshes induced a corresponding alignment of adherent cells in static culture.
The computed similarity scores for each conformer pair were stored with the translation/rotation matrix that yields the corresponding alignment.
This is a real-time preprocessing phase for detecting the possible presence and the corresponding alignment of the string in the data flow.
Alignments of the top 20 hits are extracted from the corresponding alignment dataset.
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Sequences retrieved from Blast searches were automatically integrated into the corresponding alignments and aligned using CLUSTALW, implemented in our in-house automated Blast and alignment pipeline.
The MultiFarm dataset is composed of a set of ontologies translated in different languages and the corresponding alignments between these ontologies.
Using the phylogenetic trees, we found 151 inconsistencies in the 1139 phylogenetic trees examined, which represents 13.3% of the total families studied (the set of corresponding alignments and trees can be downloaded at ftp://pbil.univ-lyon1.fr/pub/datasets/PLoS07).
For comparison, Figure 8B shows a corresponding alignment-based phylogeny computed just from the 2 kb sequences of the Amyrel gene (Da Lage et al. 2007).
To compare this tree with the corresponding alignment-based phylogeny, we followed a study of Drosophila evolution centered on the Amyrel gene (Da Lage et al. 2007): we aligned the Amyrel sequences from each organism and computed the neighbor-joining tree using clustalw (Larkin et al. 2007).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com