Datasheet

sequences. For instance, when living organisms reproduce, each of their
genes must be duplicated. In order to do this, nature doesn’t go about it the
way a photocopier would — by making an exact copy. Rather, nature sepa-
rates the DNA strands and makes
two complementary ones, thanks to the
magical two-sided structure of DNA molecules.
This double strand structure of DNA makes the definition of a DNA sequence
ambiguous: Even with our convention of reading the nucleotides from the 5’
end toward the 3’ end, you may decide to write down the bottom or the top
sequence. Convince yourself that they’re both equally valid sequences by
turning this book upside down! Thus, at each location, a DNA molecule corre-
sponds to two — totally different — sequences, related by this reverse-and-
complement operation. This isn’t complicated; simply keep it in mind every
time you work with DNA sequences.
Fortunately, most database mining programs, such as BLAST, know about this
property, and take both strands into account when reporting their results. But
some programs don’t bother — and only analyze the sequence you gave them.
In cases where both strands matter, always make sure that a complete analysis
has been performed. (We discuss these details further in Chapters 3, 5, and 7.)
Palindromes in DNA sequences
Newcomers to DNA sequence analysis are usually confused by the notion of
reverse complementary sequences. However, in due time you’ll be able to
recognize right away that the two sequences
ATGCTGATCTTGGCCATCAATG and CATTGATGGCCAAGATCAGCAT
correspond to facing strands of the same DNA molecule.
One fascinating property of DNA complementarity is the fact that regions of
DNA may correspond to sequences that are identical when read from the two
complementary strands. Figure 1-7 helps illustrate this magic trick.
T G
5' 3'
3'5'
A C
T
ACTG
A
T
A
Figure 1-7:
How two
comple-
mentary
strands can
be read the
same way.
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Part I: Getting Started in Bioinformatics
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