Sentence examples for by pairwise alignments using from inspiring English sources

The overlap of these fundamental repetitive sequences was tested by pairwise alignments using bl2seq (without filtering option; –FF) [ 28, 29].

The resulting feline and bovine inhibitor nucleotide sequences were compared by pairwise alignment using a 2-sequence BlastN [ 28].

Sequence identity was determined by pairwise alignment using the DNAMAN software package (optimal alignment; gap open penalty 10.0, gap extension penalty 5.0).

We aligned each type of tRNA and adjusted them according to their secondary structures (the alignments are the same as those used in phylogenetic analyses), and then the pairwise similarities within each type of tRNA were calculated by pairwise alignment using BioEdit (see Additional file 2).

Proteome sequences were compared using by BlastP and pairwise alignments using ClustalW and the ANI was determined by the mean percentage of nucleotide sequence identity of core proteins [ 29].

Within a set, the peptide sequences were clustered by scoring ungapped pairwise alignments using an identity matrix.

Ds values were calculated from pairwise alignments using all transcripts.

The pairwise alignments using BLOSUM62 and PfFSmat60 matrices were carried out using ApicoAlign web server (http://www.cdfd.org.in/apicoalign/) developed by us.

The L7rfo and D81Rfo sequences were compared by local pairwise alignment using the YASS program [ 43].

IS elements, transposons, and their repeat elements were identified by doing a pairwise alignment using BlastN program against the ISfinder database (http://www-is.biotoul.fr/).fr/

Canonical (-10 and -35) and Fnr promoter sequences and Shine-Dalgarno sequences were searched within 130 nucleotides upstream to the rhizobial glb genes either by using the search tool of MS Word ® or by pairwise sequence alignments using the ClustalX program (http://www.clustal.org/clustal2/).org/clustal2/