Homologous recombination (HR) is the process by which a double-strand break in DNA is repaired using an identical donor template. Despite rapid progress in identifying the functions of the proteins that mediate HR, little is known about how broken DNA finds its homologous template. This process, coined homology search, has been difficult to monitor experimentally. Therefore, we present here a c...

Homology searches for nucleotide and amino-acid sequences have been used widely to predict functions of genes and proteins when genomes are decoded and thus become a basic bioinformatics tool. Whereas usefulness of the sequence homology search is apparent, it has become increasingly clear that homology search can predict the protein function of only 50% of genes, or fewer, when a novel genome i...

To understand biological phenomena at the molecular level, such as cell-cycle, differentiation, development, proliferation, and so on, it is important to elucidate the mechanism for transcriptional control of each gene, which is involved in their phenomena. Discovery of transcription factors helps us to elucidate the new transcriptional control mechanisms that have not yet been characterized. A...

Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.

Genetic stability is a key factor in maintaining, survival, and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria, this task is accomplished by RecA proteins that are active as nucleoprotein...

MOTIVATION Many bioinformatic approaches exist for finding novel genes within genomic sequence data. Traditionally, homology search-based methods are often the first approach employed in determining whether a novel gene exists that is similar to a known gene. Unfortunately, distantly related genes or motifs often are difficult to find using single query-based homology search algorithms against ...

Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TAN...