PROBER:: oligonucleotide FISH probe design software
PROBER:: oligonucleotide FISH probe design software
复制标题
DOI：
10.1093/bioinformatics/btl273
复制
发表时间：
2006-10-01
期刊：
影响因子：
5.8
通讯作者：
Wigler, Michael
中科院分区：
文献类型：
--
作者：
Navin, Nicholas;Grubor, Vladimir;Wigler, Michael
PROBER是一种寡核苷酸引物设计软件应用程序，可设计多个引物对，用于生成可用于荧光原位杂交（FISH）的PCR探针。PROBER通过掩蔽重复的基因组序列并描绘基本上独特的区域来产生平铺寡核苷酸探针（TOP），所述区域可以被扩增以产生小的（100-2000 bp）DNA探针，所述小的（100-2000 bp）DNA探针聚集在一起将为小至单个基因的区域产生单个强荧光信号。TOP是细菌人工染色体（BAC）的替代物，其通常用于FISH，但可能是不稳定的、不可用的、嵌合的或对小（10-100 kb）基因组区域非特异性的。PROBER可以应用于任何基因组基因座，限制是基因座必须含有至少10 kb的基本上独特的区块。为了测试该软件，我们设计了许多用于基因组扩增和半合子缺失的探针，这些探针最初通过乳腺癌肿瘤的代表性寡核苷酸微阵列分析检测到。
PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.