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An open reading frame (ORF) is a reading frame that has the potential to be transcribed into RNA and translated into protein. It requires a continuous sequence of DNA which may include a start codon, through a subsequent region which has a length that is a multiple of 3 nucleotides, to a stop codon in the same reading frame.
Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames. [15] The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations. [15] Example of a six-frame translation.
Reading frames in the DNA sequence of a region of the human mitochondrial genome coding for the genes MT-ATP8 and MT-ATP6 (in black: positions 8,525 to 8,580 in the sequence accession NC_012920 [31]). There are three possible reading frames in the 5' → 3' forward direction, starting on the first (+1), second (+2) and third position (+3).
Images of all localised proteins and their bioinformatic analysis can be viewed via the ‘Results Table’ or ‘Results Images’ buttons. In addition, use the search window on the entry site to find proteins containing features or motifs of particular interest to you that have been localised in this project.
Whereas prokaryotic CDS predictors mostly deal with open reading frames (ORFs), which are segments of DNA between the start and stop codons, eukaryotic CDS predictors are faced with a more difficult problem because of the complex organization of eukaryotic genes. [3] CDS prediction methods can be classified into three broad categories: [2] [31]
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non-coding sequences: Fungi, Prokaryotes, Metazoa, Protist, Plants [41] [42] PHANOTATE: A tool to annotate phage genomes. Phages [43] SplicePredictor
Out-of-phase overlaps occurs when the shared sequences use different reading frames. This can occur in "phase 1" or "phase 2", depending on whether the reading frames are offset by 1 or 2 nucleotides. Because a codon is three nucleotides long, an offset of three nucleotides is an in-phase, phase 0 frame.