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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.
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. The nucleotide sequence is shown in the middle with forward translations above and reverse translations below. Two possible open reading ...
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.
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).
A sample DNA sequence and its respective de Bruijn Graph In a de Bruijn graph , there is a possibility of 4^k different nodes to make arrangements of a genome . The number of nodes used to create the graph can be reduced in number by considering only the k-mers found within the DNA strand of interest.
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.
Genes contain an open reading frame that can be transcribed, and regulatory sequences such as promoters and enhancers, which control transcription of the open reading frame. In many species , only a small fraction of the total sequence of the genome encodes protein.