When we investigate the relationship between viruses and their hosts, infecting virusвЂ“host pairs may only share a tiny fraction of their genomes such as CRISPR regions, and thus alignment-based approaches can potentially identify the hosts of only a small fraction of viruses. Fourth, alignment is not suitable to compare sequences of large divergence. Therefore, alignment-based approaches are not well suited to study the evolution of gene regulatory regions. Third, noncoding regions such as gene regulatory regions are not highly conserved except for some functional regions, such as transcription binding sites, and cannot be reliably aligned. Even if we can assemble the reads into long contigs, these contigs may not share long homologous regions, making it challenging to study the relationships among the genomes using alignment in such situations. However, some parts of the genomes may not be sequenced due to the stochastic distribution of the reads along the genomes and the difficulties of sequencing some parts of the genomes, especially when the coverage is relatively low. Second, in the current next-generation sequencing (NGS) era, investigators can sequence the genomes using NGS efficiently and economically. This situation makes it difficult to use alignment-based methods to investigate the relationship among whole-genome sequences. First, for whole-genome comparison, there are many duplications, translocations, large insertions/deletions, and horizontal gene transfers (HGTs) in the genomes. Although alignment-based approaches are most accurate and powerful for sequence comparison when they are feasible, their applications are limited in some situations. The most widely used methods for molecular sequence comparison are alignment based, including the SmithвЂ“Waterman algorithm ( 1), BLAST ( 2), BLAT ( 3), etc. Molecular sequence comparison is one of the most basic and fundamental problems in computational biology and has been widely used to study the evolution of whole-genome sequences and gene regulatory regions, gene function prediction, sequence assembly, and relationships among microbial communities.

Web based tools for sequence analysis