Amino acid translation program for full-length cDNA sequences with frameshift errors.
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.
Fukunishi
Y
Y
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokahama Institute, Yokohama City, Kanagawa 230-0045, Japan.
Hayashizaki
Y
Y
D001482:Base Composition; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D018387:Codon, Initiator / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D019992:Databases as Topic; D005091:Exons / Q000235:genetics; D005189:False Positive Reactions; D016368:Frameshift Mutation / Q000235:genetics*; D020407:Internet; D016013:Likelihood Functions; D009010:Monte Carlo Method; D016254:Mutagenesis, Insertional / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D014176:Protein Biosynthesis / Q000235:genetics; D012107:Research Design; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D017384:Sequence Deletion / Q000235:genetics; D012984:Software
D003062:Codon; D018387:Codon, Initiator; D018076:DNA, Complementary