Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.
Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.
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DOI：
10.1093/nar/gkp1116
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发表时间：
2010-03
影响因子：
14.9
通讯作者：
Szallasi Z
中科院分区：
文献类型：
--
作者：
Eklund AC;Friis P;Wernersson R;Szallasi Z
DNA微阵列测量易受探针和靶之间的非特异性杂交（交叉杂交）或两个靶之间的非特异性杂交（批量杂交）引起的误差的影响。搜索算法，如BLACKS，可以快速识别潜在的杂交序列。我们着手通过修改取代矩阵和空位罚分来提高BLASTING的准确性。我们生成了样品的基因表达微阵列数据，其中1%或10%的目标质量是已知序列的外源性尖峰。我们发现10%的加标在3%的探针中诱导了2倍的强度变化，其中三分之二的强度降低可能是由批量杂交引起的。这些变化与刺突和探针序列之间的相似性相关。有趣的是，即使是非常弱的相似性往往会引起探针强度的变化与10%的尖峰。使用该数据，我们优化了BLACKS取代矩阵，以更准确地鉴定对与刺突物的非特异性杂交敏感的探针。相对于默认置换矩阵，优化矩阵的特征在于A-T碱基对相对于G-C碱基对的评分降低，导致用于鉴定受影响探针的ROC曲线下面积增加5-15%。这种优化的矩阵可能是有用的微阵列探针的设计，并在其他基于BLAST的搜索杂交伴侣。
DNA microarray measurements are susceptible to error caused by non-specific hybridization between a probe and a target (cross-hybridization), or between two targets (bulk-hybridization). Search algorithms such as BLASTN can quickly identify potentially hybridizing sequences. We set out to improve BLASTN accuracy by modifying the substitution matrix and gap penalties. We generated gene expression microarray data for samples in which 1 or 10% of the target mass was an exogenous spike of known sequence. We found that the 10% spike induced 2-fold intensity changes in 3% of the probes, two-third of which were decreases in intensity likely caused by bulk-hybridization. These changes were correlated with similarity between the spike and probe sequences. Interestingly, even very weak similarities tended to induce a change in probe intensity with the 10% spike. Using this data, we optimized the BLASTN substitution matrix to more accurately identify probes susceptible to non-specific hybridization with the spike. Relative to the default substitution matrix, the optimized matrix features a decreased score for A–T base pairs relative to G–C base pairs, resulting in a 5–15% increase in area under the ROC curve for identifying affected probes. This optimized matrix may be useful in the design of microarray probes, and in other BLASTN-based searches for hybridization partners.
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DOI：
10.1073/pnas.1534744100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Mei, R;Hubbell, E;Webster, TA
通讯作者：
Webster, TA
影响因子：
3.7
作者：
Tian Z;Palmer N;Schmid P;Yao H;Galdzicki M;Berger B;Wu E;Kohane IS
通讯作者：
Kohane IS
全基因组对酿酒酵母菌株的核苷酸水平变异的分析。
影响因子：
3.7
作者：
Schacherer J;Ruderfer DM;Gresham D;Dolinski K;Botstein D;Kruglyak L
通讯作者：
Kruglyak L
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
4.4
作者：
Zhang, JH;Finney, RP;Buetow, KH
通讯作者：
Buetow, KH