An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.

Motivation: In the past few years, researchers have proposed numerous indexing schemes for searching large datasets of raw sequencing experiments. Most of these proposed indexes are approximate (i.e.

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.

The colored de Bruijn graph (cdbg) and its variants have become an important combinatorial structure used in numerous areas in genomics, such as population-level variation detection in metagenomic samples, large-scale sequence search, and cdbg-based reference sequence indices. As samples or genomes are added to the cdbg, the color information comes to dominate the space required to represent this data structure. In this article, we show how to represent the color information efficiently by adopting a hierarchical encoding that exploits correlations among color classes-patterns of color occurrence-present in the de Bruijn graph (dbg).

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches.

Comparison of the hemofiltration/molecular separation artificial kidney concept with hemodialysis: acute preclinical trials.

If adequate electrolyte adjustments are made, the only problems with the present HFMS system are the need to replenish divalent cations, add buffer, and remove the evolved CO2. Even with these deficiencies the system is portable, objectively and subjectively better than HD, and capable of being wearable in the foreseeable future.