The phrase "alignment in gene" is not correct in written English.
It may be intended to refer to the alignment of genetic sequences or genes, but it lacks clarity and grammatical structure.
Example: "The researchers focused on the alignment in gene sequences to identify mutations."
Alternatives: "gene sequence alignment" or "alignment of genes".
To avoid frameshift mutations being erroneously treated as nonsynonymous mutations, alignments in genes with potential frameshifts were trimmed to the last codon before the frameshift before running phylogenetic or population genomic analyses.
If there is more than one local alignment in a gene pair, we used the most conserved alignment.
In assessing the gene set, we define biological evidence to include biological sequence alignments used in gene prediction pipelines (transcript, peptide, protein homolog) as well as matches to InterPro domains and alignment to other bee genomes.
We filtered out connecting sequences with high scoring alignment in both genes.
Combining these two sources of information allowed us to identify 2850 SNP (1170 from Genbank alignment) in 308 genes.
This pipeline uses PASA [ 17] to generate a training set of genes from the transcript data, aligns the transcripts to the genome and uses hints generated from the alignment to assist in gene prediction.
To evaluate secondary structure-specific patterns of indel substitutions, alignments in every gene family were split based on predicted secondary structure.
To eliminate the uncertainty of the alignments in these gene regions, GBLOCKS v0.91b [ 61] was used to select those regions of the aligned sequences that are confidently aligned for analysis (Additional File 2).
The resulting amino acid alignments were then computationally reverse-translated to nucleotide alignments using the corresponding nucleotide sequences from GenBank (http://www.ncbi.nlm.nih.gov/), with the arrangement of the nucleotide triplets reflecting the protein alignment in each case (gene set).
Following sequence alignment in Mega4 [34], a gene phylogeny was inferred using the neighbor-joining algorithm and Tamura-Nei model of sequence evolution (Fig. 2), with nodal support being assessed by 1000 bootstrap replications.
