Multiple sequence alignments of partially coding nucleic acid sequences.
Multiple sequence alignments of partially coding nucleic acid sequences.
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DOI：
10.1186/1471-2105-6-160
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发表时间：
2005-06-28
影响因子：
3
通讯作者：
Stadler PF
中科院分区：
文献类型：
--
作者：
Stocsits RR;Hofacker IL;Fried C;Stadler PF
高质量的RNA和DNA序列比对是基因组序列数据比较分析的重要前提。然而，由于遗传密码的冗余性，与编码的蛋白质序列相比，核酸序列表现出更大的序列异质性。因此，在对编码核酸序列进行比对时，需要利用氨基酸序列。然而，在许多情况下，只翻译感兴趣序列的一部分。另一方面，重叠的阅读框可能编码多个替代蛋白质，可能具有间歇性的非编码部分。具体的例子是RNA病毒基因组。核酸比对的标准评分方案可以扩展到在一个或多个阅读框中同时包含翻译产品的信息。在这里，我们提出了一个多重比对工具，codaln，它实现了成对和渐进多重比对的核酸加氨基酸组合评分模型，允许对几乎所有评分参数进行任意加权。codaln的资源需求与诸如ClustalW之类的标准工具相当。我们证明了codaln对各种生物相关序列类型（噬菌体列文病毒和脊椎动物Hox簇）的适用性，并表明核酸和氨基酸序列信息的组合可以改善比对。这些反过来又提高了严格依赖于良好输入比对的分析工具的性能，例如检测保守RNA二级结构元件的方法。
High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters) and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements.
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影响因子：
64.8
作者：
GARCIAFERNANDEZ, J;HOLLAND, PWH
通讯作者：
HOLLAND, PWH
DOI：
10.1073/pnas.86.14.5459
发表时间：
1989-07-01
影响因子：
11.1
作者：
KAPPEN, C;SCHUGHART, K;RUDDLE, FH
通讯作者：
RUDDLE, FH
影响因子：
2
作者：
HEIN, J
通讯作者：
HEIN, J
DOI：
10.1098/rspb.1994.0040
发表时间：
1994-03-22
影响因子：
4.7
作者：
SCHUSTER, P;FONTANA, W;HOFACKER, IL
通讯作者：
HOFACKER, IL
影响因子：
2.9
作者：
BIEBRICHER, CK;LUCE, R
通讯作者：
LUCE, R