SynBlast: Assisting the analysis of conserved synteny information
SynBlast: Assisting the analysis of conserved synteny information
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DOI：
10.1186/1471-2105-9-351
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发表时间：
2008-08-24
影响因子：
3
通讯作者：
Prohaska, Sonja J.
中科院分区：
文献类型：
--
作者：
Lehmann, Joerg;Stadler, Peter F.;Prohaska, Sonja J.
动机：在过去的几年里，已有 20 多个脊椎动物基因组被测序，并且基因组 DNA 信息的获取速度正在迅速加快。基因重复和基因丢失事件本质上限制了仅基于序列相似性的直系同源检测的准确性。确实存在用于直系同源注释的全自动方法，但通常无法识别大基因家族中的个体成员，或者无法区分缺失数据和可追踪基因丢失。在许多情况下，可以通过包含保守的同线性信息来改善这种情况。结果：这里我们提出了旨在构建和评估本地同线性信息的 SynBlast 管道。 SynBlast 使用焦点参考基因周围的基因组区域从目标基因组集合中检索同源区域的候选区域，并根据现有的同源性证据对它们进行排名。该管道旨在作为一种工具来帮助高质量的手动注释，特别是在自动程序失败的情况下。我们以脊椎动物 Hox 和 ParaHox 簇为例，演示如何应用 SynBlast 检索直系同源和旁系同源簇。
Motivation: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.Results: Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples.