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An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

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Pozhitkov, A. E., & Tautz, D. (2002). An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification. BMC Bioinformatics, 3: 9. doi:10.1186/1471-2105-3-9.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-0E74-F
Abstract
Background: The identification of species or species groups with specific oligo-nucleotides asmolecular signatures is becoming increasingly popular for bacterial samples. However, it shows alsogreat promise for other small organisms that are taxonomically difficult to tract.Results: We have devised here an algorithm that aims to find the optimal probes for any given setof sequences. The program requires only a crude alignment of these sequences as input and isoptimized for performance to deal also with very large datasets. The algorithm is designed suchthat the position of mismatches in the probes influences the selection and makes provision of singlenucleotide outloops. Program implementations are available for Linux and Windows