ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.

Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra…

Several international conservation organizations have recently produced global priority maps to guide conservation activities and spending in their own and other conservation organizations. Surprisingly, it is not possible to directly evaluate the…

MOTIVATION: Deep sequencing has become the method of choice for determining the small RNA content of a cell. Mapping the sequenced reads onto their reference genome serves as the basis for all further analyses, namely for identification and…

Modern alignment methods designed to work rapidly and efficiently with large datasets often do so at the cost of method sensitivity. To overcome this, we have developed a novel alignment program, GRAT, built to accurately align short, highly similar…

A brain image registration algorithm, referred to as RABBIT, is proposed to achieve fast and accurate image registration with the help of an intermediate template generated by a statistical deformation model. The statistical deformation model is…

Electrospray ionization coupled with Fourier-transform mass spectrometry routinely achieves sufficiently high mass accuracy (less than or equal to 20 ppm) and resolving power (10(5)) to provide base composition and sequence information from…

Extremely fast and efficient Diels-Alder chemical ligation of furan and maleimide oligonucleotides has been carried out in aqueous buffer. It was possible to ligate three oligonucleotides simultaneously in a controlled manner with the aid of a…

Recent advances in combined HPLC/electrospray ionization-mass spectrometry provide effective new capabilities for the rapid characterization of oligonucleotides. Accurate mass measurements with errors < 0.3 Da, and determination of base and sugar…

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can…

In order to assess the significance of sequence alignments, it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment, it is empirically known that the shape of this distribution is of the…