Amino acid translation program for full-length cDNA sequences with frameshift errors
Amino acid translation program for full-length cDNA sequences with frameshift errors
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DOI：
10.1152/physiolgenomics.2001.5.2.81
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发表时间：
2001-03-08
影响因子：
4.6
通讯作者：
Hayashizaki, Y
中科院分区：
文献类型：
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作者：
Fukunishi, Y;Hayashizaki, Y
在这里，我们提出了一个氨基酸翻译程序，旨在建议实验移码错误的位置，并预测具有phred分数的全长cDNA序列的氨基酸序列。我们的程序从原始序列的低精度位置生成人工插入到人工缺失中，从而生成许多候选序列。最可能的序列的有效性（其代表实际蛋白质的可能性）通过使用根据Kozak共有序列、优选的密码子使用和起始密码子的位置计算的得分（Va）来评估。为了评估该软件，我们使用了一个数据库，其中，在612个cDNA序列，524（86%）进行773个编码序列的移码错误。我们的软件检测到并纠正了62%的总cDNA序列的移码错误的48%。移码校正的假阳性率为9%，91%的建议移码是正确的。
Here we present an amino acid translation program designed to suggest the position of experimental frameshift errors and predict amino acid sequences for full-length cDNA sequences having phred scores. Our program generates artificial insertions into artificial deletions from low-accuracy positions of the original sequence, thereby generating many candidate sequences. The validity of the most probable sequence (the likelihood that it represents the actual protein) is evaluated by using a score (Va) that is calculated in light of the Kozak consensus, preferred codon usage, and position of the initiation codon. To evaluate the software, we have used a database in which, out of 612 cDNA sequences, 524 (86%) carried 773 frameshift errors in the coding sequence. Our software detected and corrected 48% of the total frameshift errors in 62% of the total cDNA sequences with frameshift errors. The false positive rate of frameshift correction was 9%, and 91% of the suggested frameshifts were true.