MOTIVATION This document presents an implementation of the well-known Smith-Waterman algorithm for comparison of proteic and nucleic sequences, using specialized video instructions. These instructions, SIMD-like in their design, make possible parallelization of the algorithm at the instruction level. RESULTS Benchmarks on an ULTRA SPARC running at 167 MHz show a speed-up factor of two compare...

The search for local RNA secondary structures and the annotation of unusually stable folding regions in genomic sequences are two well motivated bioinformatic problems. In this contribution we introduce RNALfoldz an efficient solution two tackle both tasks. It is an extension of the RNALfold algorithm augmented by support vector regression for efficient calculation of a structure’s thermodynami...

SUMMARY The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exac...

We address the problem of sentence alignment for monolingual corpora, a phenomenon distinct from alignment in parallel corpora. Aligning large comparable corpora automatically would provide a valuable resource for learning of text-totext rewriting rules. We incorporate context into the search for an optimal alignment in two complementary ways: learning rules for matching paragraphs using topic ...

[Abstract] This paper proposed a new method to build the large scale DNA sequences search system based on web search engine technology. We give a very brief introduction for the methods used in search engine first. Then how to build a DNA search system like Google is illustrated in detail. Since there is no local alignment process, this system is able to provide the ms level search services for...

Genomic sequence databases are widely used by molecular biologists for homology searching Amino acid and nucleotide databases are increasing in size exponentially and mean sequence lengths are also increasing In searching such databases it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences only and to reduce the costs of the alignments tha...

Computer-assisted sequence comparison has become an integral part of modern molecular biology. Two types of algorithms have been used: those which search for the optimal alignment (as exemplified by the Smith-Waterman algorithm [1]), and those which identify likely alignments (as exemplified by the HMM-based “Sequence Alignment Modules” [2]). In each case, the quality of alignment is summarized...

Let N be a lattice and P ⊂ N ⊗ Z R a lattice polytope, i.e., the convex hull of finitely many points in N. Ehrhart's theorem asserts that the lattice-point counting function f P (m) := # (mP ∩ N) is a polynomial, and thus 1 + P m≥1 f P (m) t m = δ P (t) (1−t) d+1 for some polynomial δ P (t), the δ-vector of P. Motivated by the Knudsen–Mumford–Waterman Conjecture about the existence of unimodula...

David Hirshleifer joined the Merage School after serving as Kurtz Chair at Ohio State University, Waterman Professor at the University of Michigan, and as a tenured faculty member at UCLA. His recent research explores psychology and securities markets, managerial decision biases, social interactions and markets, and how firms exploit market inefficiency. Other research areas include corporate f...

A genomic database consists of a set of nucleotide sequences, for which an important kind of queries is the local sequence alignment. This paper investigates two different indexing techniques, namely the variations of GNAT trees [1] and M-trees [3], to support fast query evaluation for local alignment, by transforming the alignment problem to a variant metric space neighborhood search problem.