Sentence examples for used for pairwise alignment from inspiring English sources

The Needleman Wunsch algorithm (Needleman and Wunsch, 1970) was used for pairwise alignment.

Values used for pairwise alignments were gap opening penalty 35 and gap extension penalty 0.75.

We used the same scoring matrix as the one used for pairwise alignments of human and chimpanzee [ 24].

Protein weight matrix Gonnet 250, with Gap Opening Penalty 10 and Gap Extension Penalty 0.1 was used for pairwise alignments.

The one-to-one mapping is often used for pairwise network alignment to find the precise matching, while many-to-many mapping is more used in multiple network alignment for studying the evolutional events.

The underlying model structure used for pairwise local alignments is quite intuitive.

The ClustalW program [ 25] with standard parameters was used for pairwise and multiple amino acid sequences alignments, followed by careful visual inspection.

The same 77 alignments were used for pairwise distance calculations of proteins encoded in the C. paramecium, G. theta, and R. salina plastid genomes using the JTT matrix in MEGA 4.0.

Using BlastN for pairwise alignments of the bovine and feline inhibitor sequences, all bovine sequences align to a feline sequence with approx. 99% identity (Table  4).

The masked and annotated mouse sequence were then finally used for interspecies pairwise alignment with the sequences from the different species mentioned above using the program PipMaker [ 66].

When Blast is used for the pairwise alignment, the complexity is O(nm) where n and m refer to the lengths of the candidate and template sequences.