ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes.
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes.
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DOI：
10.1093/nar/gni005
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发表时间：
2005-01-07
影响因子：
14.9
通讯作者：
Rajakumar K
中科院分区：
文献类型：
--
作者：
Ou HY;Smith R;Lucchini S;Hinton J;Chaudhuri RR;Pallen M;Barer MR;Rajakumar K
ArrayOme是一个新的程序，可以计算基于微阵列的探针所代表的基因组的大小，并有助于识别携带大量新基因的关键细菌菌株。将在注释的参考模板上连续并通过与微阵列杂交而在测试菌株中被分类为“存在”的蛋白质编码序列（CDS）合并到IC（IC）中。然后将这些IC延伸以解释侧翼基因间序列。最后，将所有延伸IC的长度相加以产生“微阵列可视化基因组（MVG）”大小。我们使用实验和计算机生成的基因组杂交数据来测试和验证ArrayOme。当使用综合ShE.coli元阵列基因序列（6239 CDS）进行计算机杂交分析时，与真实基因组大小相比，5种测序的大肠杆菌和志贺氏菌菌株的MVG大小测定的准确度为97- 99%。然而，大肠杆菌CFT 073基因组大小被低估了14%，因为该元阵列缺乏许多CFT 073 CDS的探针。ArrayOme允许快速识别PFGE测量的基因组和MVG大小之间的不一致性，从而能够高通量鉴定富含新基因的菌株。集中在这些菌株的基因发现研究将极大地促进单个细菌物种可访问的全球基因库的表征。
ArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contiguous on annotated reference templates and classified as ‘Present’ in the test strain by hybridization to microarrays are merged into ICs (ICs). These ICs are then extended to account for flanking intergenic sequences. Finally, the lengths of all extended ICs are summated to yield the ‘microarray-visualized genome (MVG)’ size. We tested and validated ArrayOme using both experimental and in silico-generated genomic hybridization data. MVG sizing of five sequenced Escherichia coli and Shigella strains resulted in an accuracy of 97–99%, as compared to true genome sizes, when the comprehensive ShE.coli meta-array gene sequences (6239 CDS) were used for in silico hybridization analysis. However, the E.coli CFT073 genome size was underestimated by 14% as this meta-array lacked probes for many CFT073 CDS. ArrayOme permits rapid recognition of discordances between PFGE-measured genome and MVG sizes, thereby enabling high-throughput identification of strains rich in novel genes. Gene discovery studies focused on these strains will greatly facilitate characterization of the global gene pool accessible to individual bacterial species.
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影响因子：
3.2
作者：
Chen, T;Hosogi, Y;Duncan, MJ
通讯作者：
Duncan, MJ
影响因子：
3.2
作者：
Ge, H;Chuang, YYE;Ching, WM
通讯作者：
Ching, WM
DOI：
10.1073/pnas.97.26.14668
发表时间：
2000-12-19
影响因子：
11.1
作者：
Salama, N;Guillemin, K;Falkow, S
通讯作者：
Falkow, S
影响因子：
64.8
作者：
Perna, NT;Plunkett, G;Blattner, FR
通讯作者：
Blattner, FR
影响因子：
14.9
作者：
Mantri, Y;Williams, KP
通讯作者：
Williams, KP