Sentence examples for use the alignments obtained from inspiring English sources
For the UCSC sequences, we use the alignments obtained from the UCSC genome browser.
As the results presented below are robust to the choice of alignment software, we used the alignments obtained from Larracuente et al. (2008).
We used the alignments obtained during these and other searches started from other query sequences along with secondary structure predictions to construct multiple alignments for Cas7 and a number of most closely related RAMP subfamilies.
Authors state (lines 134-137): "We used the alignments obtained during these and other searches started from other query sequences along with secondary structure prediction to construct multiple alignments for Cas7 and a number of most closely related RAMP subfamilies".
Phylogenetic analysis was done on the alignments obtained using Neighbor-Joining (NJ) and Maximum Parsimony (MP) methods as implemented in PAUP* version 4.0 b10 [ 4].
The program Consensus (threshold set = 50; http://coot.embl.de/Alignment//consensus.html) was used to generate consensus sequences from the alignments obtained from A. gambiae s.s.s
For instance, we could transfer functional annotation concerning the Wnt pathway between the human and fly networks by using the alignments we obtained.
Both programs were run using the alignment files obtained from their native genome (that is, prior to liftOver).
The core functionality of AlignGraph is the extension of the contigs by reassembling them using the alignment results obtained in the previous step.
To this end, for all positive examples we used the alignment as obtained by the MCS algorithm and counted the number of times a stereo bond differs, as illustrated in Figure 3.
To test if the improved resolution with exposure filtering is due to the improved alignment of the images, we also calculated reconstructions from the noise-added data sets with total exposures of 12.6 e−/Å, 19.6 e−/Å using the alignment parameters obtained from the exposure-filtered data.
