The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (...

Many applications of next-generation sequencing technologies involve anchoring of a sequence fragment or a tag onto a corresponding position on a reference genome assembly. Positional Hashing method, implemented in the Pash 2.0 program, is specifically designed for the task of high-volume anchoring. In this article we present multi-diagonal gapped kmer collation and other improvements introduce...

Standard technologies for sequence searching do not use database indexes. These solutions can be divided into exhaustive algorithms, e.g. the Smith-Waterman algorithm [11], and heuristic ones, like BLAST [1, 2], FASTA [10], and BLAT [7]. Specialised tools for DNA matching exist, such as SIM4 [3] and SSAHA [9]. Only BLAT and SSAHA use indexing. BLAT can be used with proteins, however, its sensit...

Exact pattern searching in DNA sequence databases has applications in identification of highly conserved regulatory sequences, the design of hybridization probes, and improving performance of approximate homology searching tools such as BLAST and BLAT. We propose a new pattern searching algorithm, CompressedPunctuated-Boyer-Moore (cp-BM), to enhance exact pattern match searches of DNA sequences...

This paper presents a comparison of two strategies for cDNA/EST mapping: The seed-and-extend strategy and the fragment-chaining strategy. We derive theoretical results on the statistics of fragments of type maximal exact match. Moreover, we present efficient fragment-chaining algorithms that are simpler than previous ones. In experiments, we compared our implementation of the fragment-chaining ...