The phrase "alignments based on a" is correct and usable in written English.
It can be used when discussing various types of alignments that are determined or influenced by a specific factor or criterion.
Example: "The alignments based on a thorough analysis of the data revealed significant trends in user behavior."
Alternatives: "alignments determined by a" or "alignments influenced by a".
For comparison, the same procedure was done with conventional pair-wise alignments based on a blosum62 substitution matrix [ 2].
Over all three libraries, 283 K candidate SNPs passed the Novoalign SNP filter, in contrast to 155 K SNPs called from SOAP2 alignments based on a simple filter requiring ≥ 6 alternative calls with average alternative-allele base-quality score ≥ 20.
Last, like BLAST, computes local alignments based on a seed-and-extend technique, but it is fast because of the use of adaptive seeds thus allowing the application of classic sequence alignment techniques to the problem of mapping giga-scale sized sets of reads generated by high-throughput sequencers.
The codon alignments based on an existing protein multiple-sequence alignments for CODEML were created with the PAL2NAL [55].
A possibility of grain alignment based on a radiative torque was proposed (Dolginov and Mitrofanov, 1976); the torque was effective on irregularly-shaped grains with geometrical "helicity".
This alignment was then fitted to a second alignment based on a needle alignment of E. coli Slt70 and the RvhB1 protein from Brucella suis [116].
Both automated alignment and manual alignment based on a prior homology model for VirB2 [122] support a conserved Ala residue at the predicted signal peptide cleavage site, as well as two hydrophobic TMS regions.
Using a PSSM, it is often possible to detect very distantly related proteins which cannot be detected by the standard pairwise alignment based on a position-independent amino acid substitution matrix (AASM).
Such epitaxial alignment based on a geometrical fit between nucleating crystallites and already existing topographic features on the substrate is called "ledge directed epitaxy".
All accuracy values reported in Section 3.2 are achieved when modelling from an 'ideal' alignment, based on a structure superposition between target and template.
A pruning Perl script that is part of the pipeline was used to select closely related sequences for each alignment, based on a maximum alignment score (manuscript in preparation).
