The phrase "aligned based on their" is correct and usable in written English.
It can be used when discussing how different elements or entities are organized or coordinated according to specific criteria or characteristics.
Example: "The team members were aligned based on their individual strengths and expertise to maximize productivity."
Alternatives: "coordinated according to their" or "organized based on their".
The protein-coding DNA sequences were aligned based on their protein alignments at the web server http://www.bork.embl.de/pal2nal/[ 27].
The function F in Equation (2) estimates the log-likelihood of one pair of residues being aligned based on their context-specific information.
Since a proper alignment of the molecules prior the analysis is crucial to the successful application of these models in further studies, the molecules were aligned based on their pharmacophore features.
Nucleotide sequences of orthologous candidate genes in Hexapoda were obtained from NCBI (www.ncbi.nlm.nih.gov), ButterflyBase (http://butterflybase.ice.mpg.de) and SilkDB (http://silkworm.genomics.org.cn) and aligned based on their aa sequences to identify conserved regions.
Transfer RNA genes were aligned based on their secondary structure.
Subsequently, all assembled nucleotide sequences were aligned based on their chromosome position [ 78].
The nucleotide sequences of the 12 protein-coding genes were aligned based on the framework of their corresponding amino acid alignment using RevTrans, a web-based program for placing gaps in coding DNA based on amino acid alignments [ 54].
Here, conformations were set and molecular structures aligned based on the homologous atoms in their central and peripheral rings, as has been described in detail elsewhere [39].
The codeml program of the PAML software package was used to detect positive selection in the CYP71C subfamily [ 39]. cDNA sequences were aligned based on protein alignment by using the RevTrans 1.4 server [ 40].
The DNA sequences were aligned based on the protein alignment.
Nucleotide sequences were aligned based on amino acid alignments using MUSCLE 3.6 [ 88].
