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. 2005 Jul 26;33(13):e115. doi: 10.1093/nar/gni110

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© The Author 2005. Published by Oxford University Press. All rights reserved

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Principle of the oligonucleotide analysis program. The oligos are searched by sliding a window of 25 positions along the analyzed sequence. The 25mer is partitioned to three 8mers and a single nucleotide. 1-neighborhoods (difference of one character allowed) are constructed for each piece and compared to the precomputed index of the locations of all 8mers in the investigated data (coding regions or complete genome). Two-phase filtering program and fast bit-parallel approximate string matching algorithm are used to identify the uniqueness of the 25mers.