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SUMMARY SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it(More)
MOTIVATION Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing very long strings such as the human genome in the main memory. For example, a BWT index for the human genome (with about 3 billion characters) occupies just around 1 G bytes. However, these indexes are designed for exact pattern(More)
The Constrained Multiple Sequence Alignment problem is to align a set of sequences subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms [14], and with a(More)
MOTIVATION Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very(More)
Let <i>T</i> be a string with <i>n</i> characters over an alphabet of constant size. A recent breakthrough on compressed indexing allows us to build an index for <i>T</i> in optimal space (i.e., <i>O</i>(<i>n</i>) bits), while supporting very efficient pattern matching [Ferragina and Manzini 2000; Grossi and Vitter 2000]. Yet the compressed nature of such(More)
We consider online scheduling algorithms in the dynamic speed scaling model, where a processor can scale its speed between 0 and some maximum speed T. The processor uses energy at rate s α when run at speed s, where α > 1 is a constant. Most modern processors use dynamic speed scaling to manage their energy usage. This leads to the problem of designing(More)
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30(More)
With the first human DNA being decoded into a sequence of about 2.8 billion characters , many biological research has been centered on analyzing this sequence. Theoretically speaking, it is now feasible to accommodate an index for human DNA in the main memory so that any pattern can be located efficiently. This is due to the recent breakthrough on(More)
—The advancement of sequencing technologies has made it feasible for researchers to consider many high-throughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of(More)