ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
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DOI：
10.1093/bioinformatics/bti072
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发表时间：
2005-04-01
期刊：
影响因子：
5.8
通讯作者：
Zinic, SD
中科院分区：
文献类型：
--
作者：
Paar, V;Pavin, N;Zinic, SD
动机：GenBank数据目前缺乏α卫星高阶重复序列（HOR）注释。此外，确切的HOR共识长度迄今尚未报告。鉴于快速增长的序列数据库中的着丝粒区域，它是越来越感兴趣的是有效率的工具，从已知sequence.Results的计算识别和分析的HORs：我们开发了一个图形用户界面的方法，ColorHOR，快速计算识别的HORs在一个给定的基因组序列，而不需要先验信息的基因组序列的组成。ColorHOR基于键串算法的扩展，并提供HOR顺序和方向的颜色表示。对于关键字符串，我们使用一个强大的6 bp的字符串从一个共识α卫星和其代表性的性质进行了测试。ColorHOR算法提供了HOR的直接视觉识别（直接和/或反向互补）。更详细地说，我们首先说明了人类1号染色体的ColorHOR结果。使用ColorHOR，我们首次确定了整个人类基因组的GenBank序列的HOR注释。除了一些HORs，对应于那些先前确定的生化，我们发现新的HORs在染色体4，8，9，10，11和19。我们第一次确定了10条染色体中HORs的精确一致长度。我们建议将ColorHOR法获得的HOR序列分配纳入GenBank数据库。
Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences.Results: We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.