Method for selection of optimal microarray probes
AssigneeFebit AG
InventorsMichael Dahms, Andrea Schlauersbach, Michael Baum
Life of this patent
Estimating the term…
Abstract
The invention relates to a method for selecting a partial sequence from a nucleic acid sequence whose similarity to a given total sequence is as low as possible. More specifically, the invention relates to a method for selecting partial sequences of a given nucleic acid sequence, which are suitable for hybridization and, owing to their low similarity to said total sequence, can be used for detecting said given nucleic acid sequence.
Claims20
A method for determining the similarity of a nucleic acid sequence with respect to a given total sequence, which method comprises the steps
- (I) aligning said nucleic acid sequence with said total sequence, determining those contiguous parts of the total sequence, which correspond to a predetermined minimum degree to said sequence or to a partial sequence thereof, and
- (II) describing said correspondence of said parts of the total sequence, determined in step (I), to said nucleic acid sequence or to a partial sequence thereof in the form of scores of at least one type for segments of at least a given length and
- (III) where appropriate, merging the scores obtained in step (II).
A method for selecting nucleic acid sequences from a list of nucleic acid sequences on the basis of a total score for each sequence, which score is calculated from a set of numeric parameters for each sequence, which method comprises the steps
- (1) determining preferred values for each parameter and weighting values for each parameter and
- (2) linking each parameter to its preferred value and weighting the result to give a penalty value separately for each sequence and
- (3) linking the results of step (2) to a total score separately for each sequence and
- (4) repeating, where appropriate, steps (1) to (3) one or more times and
- (5) selecting on the basis of said total scores those sequences whose parameters deviate the least from the preferred values.
Dependencies are inferred from the claim text.