Datasheet
Because of the triplet-based genetic code, a given DNA interval, on a given
strand,
can theoretically be translated in three different ways — basically three
perspectives that are known in the field as
reading frames. Because the DNA
can be used from both strands, a total of six possible reading frames are possi-
ble for translating a DNA sequence into proteins. With very few exceptions
(found in exotic viruses), only one of these six frames is used for any given
DNA coding region. An interval of DNA sequence that remains free of STOP
(the translation of TAA, TGA, or TAG) is called an
open reading frame (ORF).
Additional complications arise from the fact that some DNA sequences are
not encoding proteins at all — and that higher organisms have large pieces
of noncoding DNA inserted within their genes. A large part of bioinformatics
is devoted to the development of methods to locate protein-coding regions
in DNA sequences, to delineate precisely where genes start and end, or where
they are interrupted by the noncoding intervals (called
introns).
DNA/RNA bioinformatics
covered in this book
Need a road map to the bioinformatic analyses that are relevant to DNA/RNA
sequences covered in this book? Here it is:
Retrieving DNA sequences from databases (Chapters 2 and 3)
Computing nucleotide compositions (Chapter 5)
Identifying restriction sites (Chapter 5)
Designing polymerase chain-reaction (PCR) primers (Chapter 5)
Identifying open reading frames (ORFs) (Chapter 5)
Predicting elements of DNA/RNA secondary structure (Chapter 12)
Finding repeats (Chapter 5)
Computing the optimal alignment between two or more DNA sequences
(Chapters 7, 8, and 9)
Finding polymorphic sites in genes (single nucleotide polymorphisms,
SNPs) (Chapter 3)
Assembling sequence fragments (Chapter 5)
Working with Entire Genomes
The first truly efficient technique to sequence DNA was discovered in
1977. In 1995, the first sequence of an entire genome (from the microbe
Hemophilus influenzae) was determined. Between these two dates, DNA-
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