A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
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DOI：
10.1186/1471-2164-9-517
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发表时间：
2008-10-31
期刊：
影响因子：
4.4
通讯作者：
Ware D
中科院分区：
文献类型：
--
作者：
Kurtz S;Narechania A;Stein JC;Ware D
精确的基因预测和计数的挑战在含有高度重复的转座因子（TE）的大基因组中进一步加剧。然而，TE在基因组进化中发挥着重要作用，并且本身也是一个重要的研究课题。重复注释，计数出现的k-mer的基础上，先前已被用来区分TE从低拷贝基因区域，但目前可用的软件解决方案是不切实际的，由于高内存要求或专业化的特定用户任务。在这里，我们介绍了Tallymer软件，一个灵活的和内存效率的收集程序的k-mer计数和索引的大序列集。与以前的方法不同，Tallymer基于增强的后缀数组。这给出了关于k聚体大小的选择的大得多的灵活性。Tallymer可以处理数十亿个碱基的大数据。我们将其用于各种应用，以研究玉米和其他植物物种的基因组。特别地，Tallymer用于索引来自玉米（B73）的一组全基因组鸟枪序列（总大小109 bp）。我们分析了宽范围k的k-聚体频率。在这种低基因组覆盖率（约0.45×）下，高度重复的20聚体占基因组的44%，但仅占所有可能的k聚体的1%。在高粱和水稻的重复片段中也发现了类似的低复杂性。当将我们的方法应用于其他玉米数据集时，高C 0 t衍生序列显示出对低拷贝序列的最大富集。在注释的TE中，最高度重复的是Ty 3/gypsy类逆转录转座子，其次是Ty 1/copia类和DNA转座子。在表达序列标签（EST）中，一个显着的部分含有高拷贝的k-mer，这表明转座子在玉米中仍然是活跃的。反转录转座子在Mo 17和McC品种很容易检测到使用B73 20聚体频率指数，表明它们的保护，尽管广泛的重排品种。在100个注释的细菌人工染色体（BAC）中，k-mer频率可以用于检测转座子编码的基因，灵敏度为92%，相比之下，使用基于重复掩蔽的重复掩蔽为96%，而两种方法均显示92%的特异性。Tallymer软件在多种应用中是有效的，以帮助玉米中的基因组注释，尽管由相对低的可用序列覆盖率所施加的限制。有关该软件的详细信息，请参见。
The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolution and are themselves an important subject of study. Repeat annotation, based on counting occurrences of k-mers, has been previously used to distinguish TEs from low-copy genic regions; but currently available software solutions are impractical due to high memory requirements or specialization for specific user-tasks. Here we introduce the Tallymer software, a flexible and memory-efficient collection of programs for k-mer counting and indexing of large sequence sets. Unlike previous methods, Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particular, Tallymer was used to index a set of whole genome shotgun sequences from maize (B73) (total size 109 bp.). We analyzed k-mer frequencies for a wide range of k. At this low genome coverage (≈ 0.45×) highly repetitive 20-mers constituted 44% of the genome but represented only 1% of all possible k-mers. Similar low-complexity was seen in the repeat fractions of sorghum and rice. When applying our method to other maize data sets, High-C0t derived sequences showed the greatest enrichment for low-copy sequences. Among annotated TEs, the most highly repetitive were of the Ty3/gypsy class of retrotransposons, followed by the Ty1/copia class, and DNA transposons. Among expressed sequence tags (EST), a notable fraction contained high-copy k-mers, suggesting that transposons are still active in maize. Retrotransposons in Mo17 and McC cultivars were readily detected using the B73 20-mer frequency index, indicating their conservation despite extensive rearrangement across cultivars. Among one hundred annotated bacterial artificial chromosomes (BACs), k-mer frequency could be used to detect transposon-encoded genes with 92% sensitivity, compared to 96% using alignment-based repeat masking, while both methods showed 92% specificity. The Tallymer software was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available. For more information on the software, see .
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影响因子：
4.3
作者：
Li R;Ye J;Li S;Wang J;Han Y;Ye C;Wang J;Yang H;Yu J;Wong GK;Wang J
通讯作者：
Wang J
影响因子：
7.4
作者：
Haberer, G;Young, S;Messing, J
通讯作者：
Messing, J
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
DOI：
10.1073/pnas.0502923102
发表时间：
2005-06-21
影响因子：
11.1
作者：
Lai, JS;Li, YB;Dooner, HK
通讯作者：
Dooner, HK