The phrase "alignment obtained from the" is correct and usable in written English.
It can be used in contexts where you are discussing the results or outcomes of a process that involves aligning elements or data.
Example: "The alignment obtained from the analysis was crucial for the project's success."
Alternatives: "alignment derived from the" or "alignment achieved through the".
Reference alignment is obtained from the structural alignment obtained from the TMalign program [43] [i.e., TM overlap].
After threading, full atomistic models of the Rev protein were generated from the template and alignment obtained from the threading studies using the MODELLER [29], [30], and NEST software tool incorporated in JACKAL 1.5 [49].
For 16S rRNA, we used cmbuild with options "--rf" and "--ere 1.4" to create an INFERNAL profile model from a hand-curated reference alignment obtained from the Ribosomal Database Project [ 30].
Degenerate forward and reverse Hr-specific primers were designed according to an amino acid sequence multiple alignment obtained from the Hr sequences available in the Swiss-Prot database: Phascolopsis gouldii (P02244), Themiste zostericola (P02245), T. dyscriptum (P02246), and Siphonosoma cumanense (P22766).
These protein alignments were then replaced with the appropriate nucleotide sequences using the RevTrans server (http://www.cbs.dtu.dk/services/RevTrans), which preserves the alignment obtained from the amino acid sequences but replaces each amino acid with the user-supplied protein coding nucleotides (Wernersson and Pedersen 2003).
For homozygous sites we use the derived allele (inferred from a six-way primate alignment obtained from the ensembl website, http://www.ensembl.org), since using the minor allele will introduce a bias due to the different sample sizes for each continental group.
As the similarity between q and a reference increases, we expect that the indirect alignment obtained from that reference will approach to the optimal one.
Local multiz alignments obtained from the PromAn server [74] were exclusively used for the promoter region of Hsp68 to define the TSS in each species.
Mouse-human base-pair identity scores were calculated using pairwise genome alignments obtained from the UCSC genome browser and the UCSC utilities axtAndBed and axtCalcMatrix.
