The phrase "alignment to process" is correct and usable in written English.
It can be used when discussing how something corresponds or fits with a specific process or methodology.
Example: "The team's alignment to process has improved our overall efficiency and productivity."
Alternatives: "conformity to process" or "adherence to process".
First, it reduces the cost of detecting false-positives as it filters out paralogs, with the exception of those caused by tandem gene duplication, and alignments to processed pseudogenes.
The redundancy setting was used because the low-complexity seeds required substantially more running time than the other seeds (>1 h compared with <1 min), and the redundancy allows their alignments to be processed in parallel in different reducers.
Furthermore, this value additionally accumulates an error gained in the process of alignment to the reference model, which we are unable to extract from the final result.
However, there are several limitations inherent to the alignment process, including alignment to repetitive regions, absent or misassembled sequence in the reference genome, and individual genetic divergence between the subject organism's genome and the reference genome [ 1].
It is possible for the true alignment to be pruned in this process, but in practice, this can be controlled by the use of heuristics and happens rarely, given long or high-quality query sequences.
To identify indels, a pipeline including SAMtools [ 55] and BCFtools (http://samtools.sourceforge.net/mpileup.shtml) was used to process alignment files.
After alignment, Samtools version 0.1.18 [ 55] was used to process the alignments files, which were visualized using the Integrative Genomics Viewer [ 56].
This is necessary as the machine-learning approach implemented in the RNAz program is not able to process alignments with more than six sequences.
To do so, the alignment algorithm is conservatively designed to process sequence reads with at most one mismatch (although this can be easily changed within the alignment tool, and may become an option in future releases).
It took GASS approximately 1.5 hours (with parallel running) to process the alignment files to achieve the structural annotations for the rhesus genome.
The SAMtools version 0.1.18 [ 36] was used to process the alignments files, which were visualized using the Integrative Genomics Viewer [ 37].
