The phrase "alignment candidates" is correct and usable in written English.
It can be used in contexts related to selecting or identifying options that fit a certain criteria or standard, often in technical or organizational discussions.
Example: "After reviewing the proposals, we identified several alignment candidates that meet our strategic goals."
Alternatives: "alignment options" or "alignment selections".
We apply substitute values for matchers that are inapplicable for the particular case and use thresholds to eliminate low-probability alignment candidates.
Then a local refinement was used starting from the alignment candidates close to the optimal solution.
In addition, we design a stochastic parallel framework that significantly speeds up the simultaneous refinement of multiple alignment candidates.
To enhance computational efficiency an approximate alignment method has been proposed to generate alignment candidates based on a fast translation-invariant rotational search [ 14, 15].
We also propose a stochastic parallel refinement method that increases significantly the efficiency for the simultaneous refinement of a set of alignment candidates.
The second stage of the CUDA-miRanda algorithm is to filter out the invalid alignment candidates as shown in Figure 6.
Sequence cDNA libraries for K. pneumoniae were aligned onto the reference genome sequence for this organism (Genbank accession number: CP000647.1 to CP000652.1), using Mosaik (http://code.google.com/p/mosaik-aligner) with the following arguments: hash size = 10, mismatach = 0, and alignment candidate threshold = 30 bp.
We used the MosaikAligner in the "all" alignment mode with a hash size of 13 and 20 bp as alignment candidate threshold, allowing a maximum of 4 mismatches.
Alignment candidate threshold (minimal alignment length to map the read) was optimized with hash size 20.
Hash size (k-mer length for alignment) was optimized first without any limitation of alignment candidate threshold.
When the alignment candidate threshold is set, only alignments reaching at least the set length are considered.
