  Pyrosequencing is among the emerging sequencing techniques, capable of
generating upto 100,000 overlapping reads in a single run. This technique is
much faster and cheaper than the existing state of the art sequencing technique
such as Sanger. However, the reads generated by pyrosequencing are short in
size and contain numerous errors. Furthermore, each read has a specific
position in the reference genome. In order to use these reads for any
subsequent analysis, the reads must be aligned . Existing multiple sequence
alignment methods cannot be used as they do not take into account the specific
positions of the sequences with respect to the genome, and are highly
inefficient for large number of sequences. Therefore, the common practice has
been to use either simple pairwise alignment despite its poor accuracy for
error prone pyroreads, or use computationally expensive techniques based on
sequential gap propagation. In this paper, we develop a computationally
efficient method based on domain decomposition, referred to as pyro-align, to
align such large number of reads. The proposed alignment algorithm accurately
aligns the erroneous reads in a short period of time, which is orders of
magnitude faster than any existing method. The accuracy of the alignment is
confirmed from the consensus obtained from the multiple alignments.
