The phrase "alignment derived from the" is correct and usable in written English.
It can be used in contexts where you are discussing the source or basis of an alignment, such as in technical, academic, or organizational discussions.
Example: "The alignment derived from the new strategy has significantly improved team performance."
Alternatives: "alignment based on the" or "alignment obtained from the".
The third method (conservation difference or CD) is based on the conservation differences between a native alignment and an alignment derived from the Z-score sequence design [ 21].
Then, every target structure was built with the MODELLER software (36), using local alignment derived from the above-described psi-blast search (37).
A sequence alignment derived from the structural superposition of HsCENP-M with HsRab1A (PDB code 4FMC, [ Dong et al., 2012]) shows that CENP-M has lost essential sequence motifs required for GTP binding and hydrolysis by small G-proteins (Vetter and Wittinghofer, 2001; Figure 3C).
The topology of the maximum likelihood tree based on a direct nucleotide alignment (edited with ALISCORE; including 12,648 positions; Additional file 5) does not differ from that based on the nucleotide alignment derived from the amino acid alignment in any strongly supported nodes.
In the maximum likelihood tree (Additional file 3) calculated based on the nucleotide alignment derived from the amino acid alignment and edited with ALISCORE [ 53, 54] comprising 12,648 positions of 49 taxa using the GTR model implemented in RAxML, a sister group relationship between brachiopods and annelids is comparatively well-supported (86% bootstrap value).
We explored further the robustness of the phylogenetic signal of the datasets against a) the alignment deriving after highly variable regions were removed with even more stringent criteria by Gblocks and b) the alignment deriving from the default settings in ClustalX.
A triphone system was then constructed based on the alignments derived from the monophone system, and a linear discriminant analysis (LDA) transform was employed to select the most discriminative dimensions from a large context (five frames to the left and right, respectively).
Individual blast alignments are clustered by linking neighboring alignments derived from the same protein in NR.
We used the EM algorithm to estimate ncRNA substitution rates from two datasets: (1) a subset of multiple alignments from release 7 of RFAM [37] whose annotated secondary structure was derived from a published source; (2) a set of pairwise alignments derived from the mix80 dataset used to parameterize the CONSAN program [38], which in turn was derived from the European Ribosomal RNA database.
The intron position information was obtained from nucleotide sequence alignments derived from the protein alignments.
PCGs and their boundaries were diagnosed via sequence comparison across alignments derived from the 68 holometabolan genome dataset.
