PubMed HealthSearch

Biomedical subjects

D C Benson

Publications and source records attributed to D C Benson.

6 recordsLinked to original sources

Fourier methods for biosequence analysis.

Novel methods are discussed for using fast Fourier transforms for DNA or protein sequence comparison. These methods are also intended as a contribution to the more general computer science problem of text search. These methods extend the capabilities of previous FFT methods and show that these methods are capable of considerable refinement. In particular, novel methods are given which (1) enable the detection of clusters of matching letters, (2) facilitate the insertion of gaps to enhance sequence similarity, and (3) accommodate to varying densities of letters in the input sequences. These methods use Fourier analysis in two distinct ways. (1) Fast Fourier transforms are used to facilitate rapid computation. (2) Fourier expansions are used to form an 'image' of the sequence comparison.

Amino Acid Sequence

Digital signal processing methods for biosequence comparison.

A method is discussed for DNA or protein sequence comparison using a finite field fast Fourier transform, a digital signal processing technique; and statistical methods are discussed for analyzing the output of this algorithm. This method compares two sequences of length N in computing time proportional to N log N compared to N2 for methods currently used. This method makes it feasible to compare very long sequences. An example is given to show that the method correctly identifies sites of known homology.

Algorithms

Energy-dispersive X-ray microanalysis of air-dried microdroplets containing a macromolecular solute.

In the preparation of microdroplets of biological fluids for X-ray microanalysis, we have found that incorporation of a macromolecular solute, dextran, to a final concentration of 1.5-2.5% retards crystal formation and produces sufficiently uniform deposits on thin films to allow droplets to be analysed without prior freeze-drying. Analyses have been carried out at 20 kV in a scanning electron microscope, using energy-dispersive spectrometry. Absorption of Na X-rays by the added solute can be significant but its effect is minimized by preparing droplets as thin as possible, and by using standards of similar composition. The minimum detectable concentrations are increased because of the extra background contribution, and for a single determination are about 6 mM for Na and 2 mM for Cl and K. These concentrations can be further reduced by measuring replicates. The reproducibility of analysis is significantly improved (to less than 5% for Na and K) over the use of calibration curves by calculating the element concentrations from a known element in the sample, chlorine. Under our analytical conditions loss of Cl did not occur. This method requires that the Cl is measured separately by microcoulometry, but eliminates the need for a range of standard droplets on the grid, and determination of the unknowns is then independent of droplet volume, beam current, counting time and magnification. We have compared, with biological samples, the results from using Cl as an internal standard with those obtained using an added standard element, cobalt. The reproducibility using Cl was approximately two-times better than that obtained with Co, probably because of unavoidable volumetric errors when the Co is pipetted separately.

Calcium