Sentence examples for by the alignment tool from inspiring English sources

Each read is then searched by the alignment tool independently.

This occurs because 32-nt sequence fragments that span the deletion site will be read as a mismatch by the alignment tool (see Figure 5A).

The Deletion_search tool of 'galign' identifies all positions in the genome that have no sequence reads, wild-type or mutant, as defined by the alignment tool output file.

Following conversion of sequence data to the 'galign' format, raw data generated by the alignment tool, Alignment_tool, is processed using a nucleotide substitution detection tool, SNP_search, and a tool for detecting other alterations, Deletion_search.

Although the presence of two or more nucleotide substitutions within a 32 nt region could be revealed by SNP_search, these regions may also be detected by Deletion_search, since most sequence reads spanning these areas will contain more than one mismatch, and will not be read by the alignment tool, giving rise to unread positions.

Underestimated mapping quality scores might cause the user to discard many accurate mappings because of the conservative estimate provided by the alignment tool.

Full-length 16S rRNA gene sequences (> 1300 bases) were added to an ARB alignment of about 28,000 small-subunit rRNA sequences by using the alignment tool ARB_EDIT of the ARB program package [ 37].

The features that are most useful in assessing mapping quality are the raw mapping qualities provided by the alignment tools and (except for Novoalign) the rate of degradation of base quality for a read.

Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can 'resurrect' many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers.

The decrease in the sensitivities of all methods can be explained by the fact that the alignment tool fails to align increasingly noisy RF reads.

The limitation of these approaches is that they must encode information in the BAM file that can be recreated by re-running the alignment tool.