Wu, T. D., Reeder, J., Lawrence, M., Becker, G. & Brauer, M. J. GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality.
Figure 5 Genomic sequence alignment of the 5′ region of Os04g27430.
Genomic sequence alignment has revolutionized our biomedical understanding.
Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species.
Based on genomic sequence alignment with EST and cDNA data, MtCBF6 and MtCBF8 have two transcript variants each, generated by intron retention/splicing events (Table 1).
Simultaneously, the genomic DNA sequences of the putative CD33rSIGLEC gene and the known CD33rSiglec protein sequence were used to conduct a protein-to-genomic sequence alignment by Wise2.
Whole genome sequence alignment analysis by using the MUMmer program revealed that extensive genomic rearrangements have taken place between ATCC 33277 and W83 (Fig. 4).
In order to visualize conserved genomic regions or chromosomal rearrangements, whole genome sequence alignments were performed by progressiveMAUVE [ 24].
By correlating phylogenomic analysis and whole genome sequence alignments, this region appears to show the typical gain and loss of sequences during the course of genomic evolution.
The conserved tammar microRNAs were found in HOX genomic sequences by alignment of human/mouse microRNAs and further confirmed by deep sequencing and miRNA mapping [ 31].
