Sentence examples for refined alignments from inspiring English sources

Sequence sets (protein or nucleotide) were aligned with Muscle [ 41], and manually refined (alignments are available upon request).

After MEGABLAST identified the sequences, we refined alignments with the bl2seq tool with a word size of seven and filtering disabled and with manual refinements.

Manually refined alignments were used as input in ProtTest v2.4 [ 57], which was set to all candidate models, a BIONJ tree, and the slow optimization strategy.

For the second-round phylogenetic analyses with 35 protostomes and deuterostomes and 2 outgroup taxa, the refined alignments (2127 aa and 4965 nt positions in length) were subjected to the two different tree-making algorithms, ML and BI.

Such refined alignments at the superfamily level can be found rarely and could be further used as reliable evolutionary models to probe various issues of conservation, length variation, structural and functional aspects of protein universe.

In-house scripts were used to parse the blat results and create input files for exonerate (Slater and Birney 2005), which generated the final, more refined alignments to the genome.

Refined alignment and sequence to structure mapping was performed in Insight II and with Slide, a interactive threading software [38].

The manually refined alignment is shown in the Supporting Information.

Delete the columns with more than 75% gaps from Ao to obtain a refined alignment A. Compute the pseudo-energy e ij for every pairing column (i, j) in A as in Equation (16).

Delete the columns with more than 75% gaps from A o to obtain a refined alignment A. Compute the pseudo-energy e ij for every pairing column (i, j ) in A as in Equation (16).

Because of its high speed and low number of artefacts evident upon visual inspection, we chose Mafft version 5, which refines alignments iteratively using pairwise alignment information.