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

Physiol Genomics. 2001 Mar 8;5(2):81-7. doi: 10.1152/physiolgenomics.2001.5.2.81.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Base Sequence
  • Codon / genetics
  • Codon, Initiator / genetics
  • Computational Biology / methods*
  • Consensus Sequence / genetics
  • DNA, Complementary / genetics
  • Databases as Topic
  • Exons / genetics
  • False Positive Reactions
  • Frameshift Mutation / genetics*
  • Internet
  • Likelihood Functions
  • Monte Carlo Method
  • Mutagenesis, Insertional / genetics
  • Open Reading Frames / genetics*
  • Protein Biosynthesis / genetics
  • Research Design
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods
  • Sequence Deletion / genetics
  • Software*

Substances

  • Codon
  • Codon, Initiator
  • DNA, Complementary