| abstract |
Methods of identifying regions of a nucleic acid sequence suitable for use as probes in nucleic acid arrays, as well as compositions of matter for practicing such methods, are provided. The subject methods include: (a) providing a set of known, undesirable probe sequences; (b) comparing a nucleic acid sequence to each member of the set; and (c) identifying regions of the nucleic acid sequence that substantially match a sequence of a member of the probe set as undesirable regions. The subject methods also include marking the undesirable regions of the nucleic acid sequence to identify regions of the nucleic acid sequence that are suitable for use as probes in a nucleic acid array. The subject invention also includes an algorithm and kits for carrying out the subject methods. Also provided are nucleic acid arrays produced with the identified suitable probes, and methods for using the same. |