Sentence examples for alignment the output from inspiring English sources

In the case of the integrin α alignment, the output from ClustalW consisted of 2383 positions and was manually edited to 1091 positions (20 sequences).

For each selenoprotein alignment, the output of the step above is a set of hits in the genomic sequence (genomic intervals), roughly corresponding to the exons of candidate selenoprotein genes (Fig. 1a).

Minor adjustments to certain regions of the alignment for optimization purposes were made based on pairwise alignments, the output saved in PHYLIP format, after which, the distances between proteins were calculated using Poisson correction and the Unrooted trees were inferred with the NJ method and then displayed using TreeView [ 39].

The pipeline (Supplementary Fig. S1) begins by running NextClip, followed by alignment of the output files for the four categories using BWA.

The input required is the sequence or alignment, and the output consists of a list of the mutations with a corresponding disease prediction presented as a pathogenicity index that ranges from 0 to 1.

After alignment, the SHRiMP output files were processed using custom R scripts and the fraction of unconverted cytosines at each potential CpG methylation site (identified in Fig. 1) was determined for each sample.

If a residue in the test sequence was aligned to a non-gap position in the reference alignment, it is correct in the output alignment if it is aligned to that same position, and incorrect otherwise.

Clicking the 'Edit alignment' button in the output page brings the user to the edit mode, where the user can change the matched atoms in the graph alignment by inserting or deleting the atom types.

To visualize the alignment results at the level of individual proteins, the output alignments from the dotplot were collected, and for each alignment, the aa positions of the alignment and Ups category of the pair of proteins were determined.

A small number of reads (20,835) were defined as chimeric by the mapping software and had two separate alignments included in the output, which in the vast majority of cases were situated on different chromosomes.

Nucleotide substitution data can be extracted from the alignment output file using the SNP_search tool.