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PubMed · 11242592

Amino acid translation program for full-length cDNA sequences with frameshift errors.

Y Fukunishi·Y Hayashizaki
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Abstract

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 (V(a)) 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.

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Base CompositionBase SequenceCodonCodon, InitiatorComputational BiologyConsensus SequenceDNA, ComplementaryDatabases as TopicExonsFalse Positive ReactionsFrameshift MutationInternetLikelihood FunctionsMonte Carlo MethodMutagenesis, InsertionalOpen Reading FramesProtein BiosynthesisResearch DesignSensitivity and SpecificitySequence Analysis, DNASequence DeletionSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Y Fukunishi, Y Hayashizaki. 2001-03-08. Amino acid translation program for full-length cDNA sequences with frameshift errors.. https://doi.org/10.1152/physiolgenomics.2001.5.2.81

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