Allowing mutations in maximal matches boosts genome compression performance

Motivation A maximal match between two genomes is a contiguous non-extendable sub-sequence common in the two genomes. DNA bases mutate very often from the genome of one individual to another. When a mutation occurs in a maximal match, it breaks the maximal match into shorter match segments. The coding cost using these broken segments for reference-based genome compression is much higher than that of using the maximal match which is allowed to contain mutations. Results We present memRGC, a novel reference-based genome compression algorithm that leverages mutation-containing matches (MCMs) for genome encoding. MemRGC detects maximal matches between two genomes using a coprime double-window k-mer sampling search scheme, the method then extends these matches to cover mismatches (mutations) and their neighbouring maximal matches to form long and MCMs. Experiments reveal that memRGC boosts the compression performance by an average of 27% in reference-based genome compression. MemRGC is also better than the best state-of-the-art methods on all of the benchmark datasets, sometimes better by 50%. Moreover, memRGC uses much less memory and de-compression resources, while providing comparable compression speed. These advantages are of significant benefits to genome data storage and transmission. Availability and implementation https://github.com/yuansliu/memRGC. Supplementary information Supplementary data are available at Bioinformatics online.

AN EXPIENCE OF THE LITTLE AUK SEXING (ALLE ALLE LINK) BY THE BEAK OUTLINES

The method of the distant field sexing of the monomorphic birds by the photographs developed initially for the White-winged Tern (Chlidonias leucopterus), turned out to be effective for the monomorphic little auks (Alle alle). Outlines of head and beak of average male and female have been prepared with an aid of Photoshop SC2 from the multiple individual outlines, based on a number of photographs of the birds of know sex (copulating birds), taken from the Internet. Males statistically significant differ from females by the heights of maxilla and mandible at the border of feathers and in the middle of the beak. However, heights cannot be treated as diagnostic due to the extensive zones of overlapping. The truly diagnostic criteria are the ratios (indexes) of the height to each other as well as the values of the discriminant functions of the mentioned ratios. Acquired thus outlines and ratios have been applied to the 49 individuals of the little auks on the photographs. Their sex was known to the examining party, but not to the author. The maximal match of the outlines to the specimen on the photograph showed its possible sex. The subsequent check of the data showed 100% correct sexing. Similar level of the correct sexing has been reached by using the discriminant equations, based both on a number of measurements of the beak (significantly different in the opposite sexes) and the ratios between these measurements, showing the degree of their robustness and expression of certain characters of the beak (gonys, nail, culmen, etc.). The mentioned method is useful not only for the monomorphic species of all the ages and in various seasons, but also for the dimorphic species in the periods, when distant sexing is difficult (non-breeding, juvenile and nestling plumage). About 570 species, studied so far, proved the sensitivity of the sexing method.