Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared
characteristics. Most genetic string matching methods are based on the edit-distance model, which does not provide
alignments for inversions and translocations. Recently, a heuristic called the Walking Tree Method [2, 3] has been...
The computational identification of gene Transcription Start Sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are...
The meaning of biological sequences is a central problem
of modern biology. Although string matching is well understood
in the edit-distance model, biological strings
with transpositions and inversions violate this model's
assumptions. To align biologically reasonable strings, we
proposed the Walking Tree Method [4,5,6,7,8], an
approximate string alignment method that...
Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...