The phrase "alignment template" is correct and usable in written English.
It can be used in contexts where you are referring to a document or tool that helps ensure consistency or agreement in a particular process or design.
Example: "Before we proceed with the project, let's review the alignment template to ensure all team members are on the same page."
Alternatives: "consistency framework" or "standardization guide."
All 16S sequences from completed genomes and all Clostridiales-type strains in the Ribosomal Database Project (Cole et al. 2009) were aligned to the Greengenes reference alignment template using PyNAST (Caporaso et al. 2010) and masked to include only the phylogenetically informative sites, resulting in an alignment of 2,217 sequences and 1,287 sites.
To align a candidate sequence with an alignment template in PO-MSA format, we extend the dynamic programming recursion from the Needleman Wunsch algorithm.
The NAST algorithm [29] tries to align new sequences against a precalculated multiple alignment template, and has been integrated into many commonly used 16S rRNA analysis tools such as Mothur [11] and GreenGenes [31].
To minimize redundancy between proteins reported in the three individual iTRAQ sets and to ensure consistency of reported isoforms from one set to the next, the results of the three sets were aligned using a Microsoft Excel-based (Microsoft, Redmond, WA, USA) protein alignment template as described elsewhere [ 19].
After structural alignment, template will be mapped to query.
Most phylogeny [20], [21], community distance estimates [11], [22], and abundance distributions [23] [25] ultimately rely on input from a multiple alignment to compute sequence distances within a consistent alignment template.
For reason #2 above, don't use alignment templates that have rotations between the voxel indices i,j,k) and the coordinates (x,y,z).
Libraries were sequenced using two methods: with Roche 454 Titanium on pooled RNA from all 14 tissues to generate long reads to serve as alignment templates; and with the Illumina Genome Analyzer to generate high sequence coverage and transcript counts (for use in analyses to be published separately).
The model quality of TBM depends on sequence-template alignment and template selection, both of which are challenging when only distantly related templates are available for a protein sequence under prediction.
We manually curated the alignment between template and LGI1, keeping in consideration the secondary structure prediction.
The amino acid sequences were aligned by ClustalX and the nucleotide sequence alignments were generated based on the amino acid sequence alignment as template using RevTrans program [34].
