The phrase "alignment we first" is not correct and does not form a coherent expression in written English.
It appears to be an incomplete thought and lacks clarity, making it difficult to determine its intended use.
Example: "In our project, alignment we first need to establish before moving forward."
Alternatives: "we prioritize alignment" or "alignment is our first step".
In order to create the multiple alignment, we first retrieved 108 human TK gene records from EntrezGene by querying for domain cd00192 [26].
To evaluate a given alignment, we first evaluate the likelihood of the coding model as follows.
For the computation of a single ExpLoc alignment, we first computed the mfe structure with RNAfold of each sequence and input the two RNAs to ExpaRNA.
To calculate false discovery rate (FDR) of term alignment, we first create n ontologies with the same structure as the inferred ontology O i but with all gene labels randomly permuted.
To generate whole-genome multiple alignments, we first aligned the reference genome to each target genome in a pairwise manner.
To investigate the effect of different query alignments, we first repeated the analysis using query repeat alignments that had been further optimised.
To build these four alignments, we first used the ITS sequences of full length, including any fringe residues of 18S and 28S, to construct "whole ITS" alignments with both Clustal W and SATé.
The fitting algorithm proceeds as follows: Given N codon alignments, we first reconstructed a neighbor joining tree [23] using the Tamura-Nei nucleotide distance metric [24] separately for each alignment.
For a given set of sequence alignments, we first estimate the individual gene trees using traditional phylogenetic methods.
Regarding phylogenetic analyses, for each one of the multiple sequence alignments we first used ModelTest 1.3 [ 36] to determine the best candidate substitution rate matrix for maximum likelihood inference.
To assess the impact of sequence divergence on multiple alignment accuracy we first compared the alignments from Muscle with the true INDELible alignments.
