Abstract
BackgroundLarge nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.ResultsWe present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divide and conquer approach is then applied to break the sequences into fragments that can be aligned independently by an external alignment program. These partial alignments are assembled together to form a complete alignment of the original sequences.ConclusionsMISHIMA provides improved performance compared to the commonly used multiple alignment methods. As an example, six complete genome sequences of bacteria species Helicobacter pylori (about 1.7 Mb each) were successfully aligned in about 6 hours using a single PC.
Highlights
Large nucleotide sequence datasets are becoming increasingly common objects of comparison
We found that knowing the number of occurrences of each k-tuple in the original sequence dataset is not enough to efficiently decide which k-tuples are more likely to represent the local homology
Human mtDNA genomes Complete human mitochondrial DNA genome sequences were used as an example of very closely related sequences
Summary
We present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divide and conquer approach is applied to break the sequences into fragments that can be aligned independently by an external alignment program. These partial alignments are assembled together to form a complete alignment of the original sequences
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have