The phrase "as reference alignment" is correct and usable in written English.
It can be used in contexts where you are discussing the alignment of data, concepts, or frameworks in relation to a reference point or standard.
Example: "The results were analyzed as reference alignment to ensure consistency across the datasets."
Alternatives: "for reference alignment" or "in reference alignment".
Among the obtained alignments, those with TM-scores >0.6 for Fr-TM-align and those with Z-scores >2 for DaliLite were used as reference alignments, respectively.
To assess the alignment quality, we compared sequence alignments with the structural alignments generated by Fr-TM-align (Pandit and Skolnick, 2008), which allows flexible alignments, and DaliLite (ver. 3.3) (Holm et al., 2008) as reference alignments.
The sequences for the hypothetical target species, Primate and Rodent, were removed from the simulated alignments and the rest of the aligned sequences were used as the reference alignment (RA).
To reduce the complexity, we first use the 1-best phone transcription generated by the LVCSR decoder as a reference alignment to divide the whole speech utterance into time slots, and then fill each slot using N-best phone hypotheses.
However, we only use the first alignment generated by the structure alignment tools for a protein pair as the reference alignment.
Figure 7 presents the structure of the reference alignment, as well as alignments generated by MSARC, Probalign and MSAProbs.
Sequences were aligned using the Silva reference alignment as a template and potentially chimeric sequences were eliminated using the UChime algorithm34.
For each alignment tool, Figure 4 shows the dependency of alignment quality on sequence identity across k2; for each benchmark instance, the quality is measured as similarity to the Rfam-derived reference alignment reported as sum-of-pairs score (SPS) by compalignp (Wilm et al., 2006).
Sequences were aligned to the 16S rRNA gene, using as template the SILVA reference alignment (Pruesse et al., 2007), and the Needleman-Wunsch algorithm with the default scoring options.
Bowtie and BWA outperform previous read mappers, such as MAQ and SOAP, for contiguous reference alignment in terms of speed and accuracy (Table 1).
