OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
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DOI：
10.1186/1751-0473-2-5
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发表时间：
2007-12-01
影响因子：
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通讯作者：
Wildman, Derek E.
中科院分区：
文献类型：
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作者：
Liu, Guozhen;Uddin, Monica;Wildman, Derek E.
背景：多个物种基因组序列数据的快速积累为DNA序列进化的检测提供了强有力的机会。系统发生树构建和基于密码子的自然选择测试是用于检测蛋白质编码序列中重要功能进化变化的流行工具。这些分析通常需要多个DNA序列比对，以维持每个推定的正向同源序列集合的正确阅读框架。由于这一功能是不可用的，在大多数比对工具，密码子阅读框往往必须手动检查之前，进化analysis.Results：在这里，我们报告了一个在线密码子保留的比对工具（OCPAT），自动生成多个序列比对的任何列表的人类基因ID和他们的推定的直系同源物从其他脊椎动物四足动物的基因组的编码序列。OCPAT被编程为从基因组中提取推定的直向同源基因，并将直向同源基因与所有物种中保持的阅读框架进行比对。OCPAT还通过修剪每个基因的5'和3'末端的最可变比对区域来优化比对。比对的结果输出以几种格式返回，这有助于通过适当的可用软件进行进一步的分子进化分析。对齐通常是稳健和可靠的，保持正确的阅读框架。该工具可以作为蛋白质编码基因序列的比较基因组分析的第一步，包括系统发育树重建和自然选择的检测。我们使用OCPAT比对了20，658个人类RefSeq mRNA。大多数比对缺失的序列（S）从至少一个物种，然而，功能注释聚类的类似于1700转录本，可与所有物种的显示，参与多亚基蛋白复合物的基因是高度保守的。结论：OCPAT程序有利于大规模的进化和系统发育分析的整个生物过程，途径和疾病。
Background: Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.Results: Here we report an online codon-preserved alignment tool (OCPAT) that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s) from at least one species; however, functional annotation clustering of the similar to 1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved.Conclusion: The OCPAT program facilitates large-scale evolutionary and phylogenetic analyses of entire biological processes, pathways, and diseases.