Abascal Federico, Zardoya Rafael, Posada David
Departamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.
Methods Mol Biol. 2009;537:233-42. doi: 10.1007/978-1-59745-251-9_11.
There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis.
大多数生物使用一种标准遗传密码，但也存在例外情况，即特定密码子被翻译为不同的含义，也就是作为不同的氨基酸。因此，表征生物体的遗传密码是正确分析和翻译其蛋白质编码基因的关键步骤。在后生动物线粒体基因组的情况下，这种表征尤为重要，原因有两个：第一，其中出现了许多变体密码；第二，线粒体数据经常用于进化研究。变体密码通常通过比较序列分析来发现。给定一个蛋白质比对，如果给定物种的某个特定密码子出现在其他物种中经常发现特定氨基酸的位置，那么最有可能的假设是该密码子在该物种中被翻译为该特定氨基酸。此前，我们已经表明，只要比较中包含足够的分类单元和位置，这种方法就会非常可靠，并且我们已经在网络服务器GenDecoder（http://darwin.uvigo.es/software/gendecoder.html）中实现了该方法。在本章中，我们描述了GenDecoder所使用方法的基本原理及其通过实例的用法，强调了分析过程中可能出现的潜在问题。
