To discriminate between these possibilities as the cause for the greater sequence identity between paralogues, we compared the codon usage of conserved (and identical) amino acids in group 1, 2 and 3 genes.
To determine whether repeat sequence abundance changes between developmental stages, we compared the median percentage abundance between sequences from the same developmental stage to that across all sequences (Table 2).
To determine small genetic differences between these strains we compared a composite sequence from NCM4139, NCM4287, and NCM4370, which had the highest sequence coverage, to MG1655 computationally as described in Materials and Methods (Fig. 1).
To investigate other possible molecular causes that might be responsible for the differences in transcriptional activity between isolates 'A' and 'B', we compared sequences of known transcriptional regulators and some of their expected target promoters in two isolates.
To better understand the sequence diversity between these mollusk species, we compared the L. stagnalis cDNA sequences (7712 sequences with an average length of 862 nucleotides) with the EST sequences from A. californica reported by Moroz et al [ 38].
To identify the responsible sequences in the SD region, we compared the sequences between the O. marmoratus X and Y chromosomes, and detected 55 Y-specific mutations, comprising 37 SNPs and 18 indels.
To reveal the genetic differences between MEAM1 and MED, we compared the sequence variations between them and identified a number of orthologous genes that show signs of diversifying natural selection.
Therefore, to assess whether there was greater divergence between species within s-DMRs, we compared the sequence similarity between the s-DMRs and the total background set of peaks that these were identified from.
To investigate the relationship between sequence conservation and thermodynamic stability, we compared the thermodynamic stability of conserved and non-conserved pre-miRNAs from human, mouse, and chicken genomes, with special emphasis on ultra stable and unstable pre-miRNA sequences.
To determine the genetic basis for the phenotypic difference between 81116AI2- and 81116AI2+, we compared the sequences of the luxS gene in the two variants.
