Sentence examples for using the pairwise alignment from inspiring English sources

The amino acid sequences of 105 orthologous genes were aligned using the pairwise alignment program (ClustalW) and the amino acid replacements were obtained in the form of a matrix, using a program developed in-house in Visual Basic.

To locate the duplication breakpoints for large human gene pairs, sequences within 200 kb flanking region (800 kb for few pairs) of each gene were aligned using the pairwise alignment tool LASTZ [ 64].

Sequences were aligned in ClustalW [ 70] using the pairwise alignment algorithm and alignments were manually controlled and improved locally.

The alignments of orthologous sequences of three groups were created separately using the pairwise alignment program ClustalW and only the gap-free aligned regions of length >100 residues were considered to avoid any spurious short-alignment regions.

Alignments of protein sequences were done using the pairwise alignment algorithms EMBOSS [60], provided by EMBL-EBI (http://www.ebi.ac.uk), and bl2seq [61], provided by NCBI (http://blast.ncbi.nlm.nih.gov).nih.gov

A distance matrix is generated for each block using the pairwise alignment algorithm.

For BLAST local sequence alignment, we used NCBI BLASTN (Altschul et al., 1997), with default parameters except for a word length of W=6 and an E-value cut-off of 1.0, and used the pairwise alignment with the lowest E-value to identify the nearest neighbor among any of the individual training set sequences.

We used the pairwise alignments reported by BLASTP to guide the construction of alignments of the corresponding coding regions, inserting in-frame gaps where necessary.

To address this issue, I used the pairwise alignments of human and mouse orthologues to produce an occupancy matrix for positions -8 to +10 of the initiator [see Additional file 4].

annuus, NC007977; L. sativa, DQ383816; P. argentatum, GU120098; G. abyssinica, EU549769 and J. vulgaris, HQ234669), were aligned using the pairwise automatic alignment tool in MacClade 4.06 with further adjustment by hand.

We also found a lack of detectable DNA sequence relationship between the nub and pdm-2 noncoding sequences (both conserved and less conserved sequences) using the pairwise sequence alignment tools Blastn [ 18] and cis-Decoder [ 8].