O'Reilly logo

Beginning Perl for Bioinformatics by James Tisdall

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

Reading Frames

The biologist knows that, given a sequence of DNA, it is necessary to examine all six reading frames of the DNA to find the coding regions the cell uses to make proteins.

What Are Reading Frames?

Very often you won't know where, in the DNA you're studying, the cell actually begins translating the DNA into protein. Only about 1-1.5% of human DNA is in genes, which are the parts of DNA used for the translation into proteins. Furthermore, genes very often occur in pieces that are spliced together during the transcription/translation process.

If you don't know where the translation starts, you have to consider the six possible reading frames. Since the codons are three bases long, the translation happens in three "frames," for instance starting at the first base, or the second, or perhaps the third. (The fourth would be the same as starting from the first.) Each starting place gives a different series of codons, and, as a result, a different series of amino acids.

Also, transcription and translation can happen on either strand of the DNA; that is, either the DNA sequence, or its reverse complement, might contain DNA code that is actually translated. The reverse complement can also be read in any one of three frames. So a total of six reading frames have to be considered when looking for coding regions , that part of the DNA that encodes proteins.

It is therefore quite common to examine all six reading frames of a DNA sequence and to look at the resulting protein translations ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required