Sentence examples for we implemented an alignment from inspiring English sources
We implemented an alignment approach that takes these nucleotide misincorporation patterns into account (SOM Text 3) and aligned the Neandertal sequences to either the reference human genome (UCSC hg18), the reference chimpanzee genome (panTro2), or the inferred human-chimpanzee common ancestral sequence (SOM Text 3).
In order to identify the similarity of the nrESS, we implemented a pairwise alignment algorithm based on the Dynamic Programing Needleman and Wunsch (NW) algorithm as described in reference [ 46].
To reduce the run time for pairwise alignments, we implemented an option called fast mode.
We implemented a similar multiple alignment program in MATLAB to test additional scoring metrics and methods of guide tree construction.
To overcome the above mentioned difficulties, and to deal with other situations that cause problems for alignment programs, we implemented a semi-automatic anchored alignment approach.
Instead, we implemented a three-dimensional dynamic programming alignment (Lipman et al, 1989; Durbin et al, 1998) that simultaneously maximizes the similarity between Neandertal, human, and chimpanzee sequences.
To reduce the incidence of false positives due to poor alignments, we implemented a filtering method based on the consistency of matches and mismatches on both sides of the exon-exon junction, essentially requiring that at least one read have a match to the genome at all 11 bp on both sides of the junction.
Moreover, in this study, we implemented a procedure based on the local alignment software CHAOS, which may still miss some conserved segment candidates.
As an alternative, in which fewer alignments are discarded, we implemented a simple hill-climbing approach.
We have implemented a simple alignment tool and the features are extracted from UniProtKB flat files and PDB records and the user can easily identify the features of interest in the amino acid sequence.
CLUSS implements an alignment-independent similarity measure [29] and therefore was run directly with the C. elegans protein sequences as input.
