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Based on preliminary phylogenetic analyses, 25 representative taxa were selected for compilation of PAL genes, sequence alignment and tree reconstruction.
In order to assign protein functions to the 13,120 predicted genes, sequence alignment analysis by pairwise comparison between A. oryzae and closely related fungi was performed.
Additionally, the MeSH profiles were inspected qualitatively by reading the terms and identifying concepts, which describe the aspects, these terms have in common (e.g. "DNA", "Genes", "Sequence alignment" could be summarized by the concept "Molecular Biology").
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In these three coding genes sequences alignment was based on the inferred amino acid sequence.
The gene sequence alignment of flavin nucleotide binding domain indicates that this is a highly conserved domain across many azoreductases.
The test for positive selection was conducted using a likelihood-based method, where the likelihood of different evolutionary models is computed given a gene sequence alignment and a reconstruction of the phylogenetic history of the genes.
Additional file 3: TAAR gene sequence alignment.
File_3 includes each gene sequence alignment of coding region among the three species with guinea pig.
16S rDNA gene sequence alignment has been used as the reference method for mycobacterial species identification.
(ZIP 342 kb) Additional file 3: File_1 and File_2 include each gene sequence alignment of non-coding and coding region among T.
The hypothesis that the flowering time QTL on SBI-10 was caused by alleles of CONSTANS/Hd1 was investigated further through gene sequence alignment and analysis of colinearity.
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