Locality-sensitive hashing has been applied in several problems in bioinformatics to quickly search large sequences by examining the n-grams of the sequences. We observe in these application a bias in the random generation of hashes and define an effective equivalence for hashes that generate nearly identical results. Methods that address these two points demonstrate an improvement to the rate ...

The aim of this paper is to study certain properties of the weight spectral sequences of Rapoport-Zink by a specialization argument. By reducing to the case over finite fields previously treated by Deligne, we prove that the weight filtration and the monodromy filtration defined on the l-adic étale cohomology coincide, up to shift, for proper smooth varieties over equal characteristic local fie...

RNA sequences have been discovered that mediate the growth of hexagonal palladium nanoparticles. In vitro selection techniques were used to evolve an initial library of approximately 10(14) unique RNA sequences through eight cycles of selection to yield several active sequence families. Of the five families, all representative members could form crystalline hexagonal palladium platelets. The pa...

The diversity of sulfate-reducing bacteria (SRB) in brackish sediment was investigated using small-subunit rRNA and dissimilatory sulfite reductase (DSR) gene clone libraries and cultivation. The phylogenetic affiliation of the most commonly retrieved clones for both genes was strikingly similar and produced Desulfosarcina variabilis-like sequences from the inoculum but Desulfomicrobium baculat...

Benzoyl-CoA is the signature central metabolite associated with the anaerobic metabolism of a diverse range of compounds such as humic acid, lignin, amino acids, and industrial chemicals. Aromatic chemicals with different upstream degradation pathways all funnel into the downstream benzoyl-CoA pathway. Different genes encoding enzymes of the benzoyl-CoA pathway could be used as biomarkers for t...

The main idea of Regular Sequences of Similar Algorithm based on Sparse Linear (HR Algorithm) is to calculation the near optimal solution from the solution of sparse integer programming model. The advantages of HR algorithm are simplifying the problem of huge solution space of integer programming, reducing the number of goal constraints, and turning the problem into a simplified integer program...

Visualizing and understanding large complex temporal datasets can be difficult and confusing because of the structure of events and event sequences. We introduce a novel Temporal Search and Replace tool that lets users easily and intuitively group and simplify related events sequences or repeated event patterns. The features in the tool were evaluated with a usability study of nine participants...

Multiple sequence alignment program, ClustalW, is time consuming, however, commonly used to compare the protein sequences. ClustalW includes two main time consuming parts: pairwise alignment and progressive alignment. Due to the irregular computation based on tree in progressive alignment, available parallel programs can not achieve reasonable speedups for large scale number of sequences. In th...

A novel DNA bioassay-on-chip using surface-enhanced Raman scattering (SERS) on a bimetallic nanowave chip is presented. In this bioassay, SERS signals were measured after a single reaction on the chip's surface without any washing step, making it simple-to-use and reducing the reagent cost. Using the technique, specific oligonucleotide sequences of the dengue virus 4 were detected.

Desulfuribacillus alkaliarsenatis AHT28T is an obligately anaerobic, sulfur- and arsenate-reducing haloalkaliphile that was isolated from Russian soda lake sediments. Here, we present the 3.1-Mb draft genome sequence for this strain, consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding sequences.