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

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokahama Institute, Yokohama City, Kanagawa 230-0045; Genome Science Laboratory, RIKEN Tsukuba Institute, and Core Research of Evolutional Science and Technology, Japan Science and Technology Corporation, Tsukuba City, Ibaraki 305-0074, Japan

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.

phred score; Kozak consensus; codon usage; initiation codon; base-call error

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