Sentence examples for edited the alignment from inspiring English sources

We combined the protein sequences from both AVRK1 and AVRA10 analyses, aligned them with muscle [ 59] and edited the alignment using jalview [ 61].

When this occurred in the internal part of the element, we manually edited the alignment to remove the columns corresponding to the repeat.

We subsequently manually edited the alignments by realigning the first 45 bp of short sequences ("edited" matrices).

To ensure comparable data analyses, and to remain conservative in subsequent tests for positive selection, we applied several criteria to remove highly divergent sequences: we manually edited the alignments in BioEdit, removing unalignable N- and C- termini up to the first set of completely conserved amino acid residues.

Concatenated sequences of these 175 genes were aligned using ClustalX v. 10.0.2 [ 40] or Muscle v. 3.6 [ 41] and Gblocks v. 0.91b [ 42] was applied to edit the alignment to remove gaps and poorly aligned regions.

A GUI for editing the alignment results is also implemented in this software.

After editing the alignment and clicking the 'Save & Predict' button, the user can carry out the EC number prediction again based on the refined RDM pattern.

Some features of BoulderALE include the annotation and evaluation of an alignment based on isostericity of Watson Crick and non-Watson Crick base pairs, alonon-Watson Crickapsing (horizontally and vertically) of the alignment, while maintaining the abasety to edit the alignment.

Using the secondary structure (including non-Watson Crick base pairs), it is thenon-Watson Crickghlight base pairs it the secondary structure that do or do not match is thenalignment, and the user can then edit the alignment to opossibletois matchighlight

Protein multiple sequence alignments were built using MUSCLE with default parameters [ 104] and Jalview [ 105] was subsequently employed to inspect and edit the alignments.

We believe the poor representation of 3R duplicates in our trees is partly a reflection of the strict criteria we used when editing the alignments of sequences from incomplete or poorly annotated genome databases.