Sentence examples for return alignment from inspiring English sources

To compare the performance of different methods, BLAT, SSAHA2 and FACS were used to examine both datasets; these comparative methods were chosen as they represent conventional long DNA read alignment methods, although in this study FACS does not return alignment coordinates.

The first alignment is based on NAST which removes non-16S pyrotags in the returned alignment.

The settings used to run each method were: PSI-BLAST was run using NCBI NR database-added 534 query sequences, with the settings of a maximum number of 20 iterations (-j option), 0.0005 e-value threshold to include sequences for a profile construction at each iteration (-h option), and 1000 e-value threshold for returned alignment in the final iteration (-e option).

As our software makes no assumptions based on prior biological or biochemical knowledge, the end-user is able to navigate the full set of returned alignment summaries (strength of hit as E-value and bit score, subject accession numbers, etc).

The tool returns alignments in HTML format and a summary of the output can be downloaded.

In some instances, a single queried sequence returned alignments with multiple targets.

The underlying SSWAP semantic web service accepts parameterization of gapped alignments, expectation and extension thresholds, word size settings, and limits on maximum hits and returned alignments.

Careful inspection of returned alignments led us to infer the presence of at least 13 mitochondrial fragments into the nuclear genome.

To calculate the posterior probabilities efficiently, we use the following intermediate values: Then Equation (1) can be rewritten as: (2) Step 1 inevitably uses a cut-off: it returns alignments with score.

For both species, BLAST search produced numerous significant alignments with the anticodon stem of tRNA-Cys of mites and other arachnids, crustaceans, and insects (Additional file 5, 27-28); for D. farinae only, BLAST also returned alignments with tRNA-Ala, but they were consistently worse than those with tRNA-Cys.

The mapping tool was configured to return all alignment hits by setting the seed length to 28 bp.