However, the promoter regions only account for a limited number of locations where transcription factor binding sites can occur, and multiple genome alignments often cannot align binding sites with their true counterparts because of the short and degenerative nature of these transcription factor binding sites.
However, current multiple genome alignments may not be able to align TFBSs and their orthologous counterparts well.
To detect triplets of conserved sequence segments among the three species, multiple genome alignments were performed using the progressiveMauve aligner [ 44], with the following parameters: seed weight of 20 and use a family of spaced seeds.
The problem of multiple genome alignments and in general, the problem of multiply aligning non-transcribed sequences, has voluntarily been excluded from the scope of this review.
In the present work, we describe a new method to construct positional homology multiple genome alignments that extends our previous method [9] to aligning regions conserved in subsets of the genomes.
Furthermore, the CRM regions may be shuffled in evolution and cannot be aligned with their true orthologous CRM regions in multiple genome alignments.
In order to provide further evidence for the identification of Cucurbitaceae orthologs, we performed multiple genome alignments of C. melo, C. lanatus and C. pepo genomic regions harbouring MLO genes.
The multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies.
Recently, we developed RNAcode, a gene prediction program that uses the principle of comparative genomics [ 15] to detect protein-coding genes in multiple genome alignments [ 16].
Multiple genome alignments are downloaded from UCSC Genome Browser [22].
