"aligned based on" is correct and usable in written English.
You can use it when talking about something being arranged or organized according to a set of criteria or rules. For example, "The report was aligned based on the latest research and industry trends."
The DNA sequences were aligned based on the protein alignment.
Nucleotide sequences were aligned based on amino acid alignments using MUSCLE 3.6 [ 88].
The nucleotide sequences were aligned based on amino acid alignment using PRANK by applying the TranslatorX perl script [ 43].
The protein-coding DNA sequences were aligned based on their protein alignments at the web server http://www.bork.embl.de/pal2nal/[ 27].
Nucleotide sequences of selected subgroups of Rab proteins were aligned based on corresponding amino acid alignments.
All PCGs were aligned based on amino acid sequence alignments in MEGA version 4.0 [ 41].
Prank [ 80] was used to conduct codon alignment, in which two protein sequences were aligned first and then DNA sequences were aligned based on the corresponding protein alignments.
A data set comprising genomic sequences of five chromosomal segments from two homoeologous regions of the maize genome (resulting from WGD), one from sorghum and one from rice, have been previously aligned based on collinear genetic markers (Fig. 1).
The function F in Equation (2) estimates the log-likelihood of one pair of residues being aligned based on their context-specific information.
The remainder of the sequences is then aligned based on the consistency constraints given by these pre-aligned positions.
Expanded view (middle) of the linker domains that are aligned based on the stretch (gray box) for which the sequence alignment is shown on the right.
