BLAST

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Evolution

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27

But what if you translate it from the second nucleotide? You get a different protein

sequence (note that the fractional codon AC at the end of the DNA translates to thre-

onine no matter what the next nucleotide is):

LYHT

Because codons are three nucleotides long, you can translate DNA in three different

reading frames. Since DNA is double stranded, there are really six reading frames for

every piece of DNA. So if someone hands you a DNA sequence and asks you to

translate it, you may have a little trouble.

Evolution

BLAST works because evolution is happening. Biological sequences show complex

patterns of similarity to one another. In this regard, they mirror the external mor-

phologies of the organisms in which they reside. You’ll notice that birds, for exam-

ple, show natural groupings. You don’t have to be a biologist to see that ducks,

geese, and swans comprise a reasonably natural group called the waterfowl, and that

the similarities between ducks and geese seem too great to explain by mere coinci-

dence. Biological sequences are no different. After all, the reason why ducks look like

ducks and geese look like geese is because of their genes. Many molecular biologists

are convinced that understanding sequence evolution is tantamount to understand-

ing evolution itself.

Sequences change over time due to three forces: mutation, natural selection, and

genetic drift. If you use BLAST, it’s important to understand these forces because

Figure 2-3. Standard codon translation

T

TTT Phe (F)

TTC "

TTA Leu (L)

TTG "

T

C

TCT Ser (S)

TCC "

TCA "

TCG "

A

TAT Tyr (Y)

TAC

TAA Ter

TAG Ter

G

TGT Cys (C)

TGC

TGA Ter

TGG Trp (W)

CTT Leu (L)

CTC "

CTA

CTG "

C

CCT Pro (P)

CCC "

CCA "

CCG "

CAT His (H)

CAC "

CAA Gin (Q)

CAG "

CGT Arg (R)

CGC "

CGA "

CGG "

A

G

ATT IIe (I)

ATC "

ATA "

ATG Met (M)

ACT Thr (T)

ACC "

ACA "

ACG "

AAT Asn (N)

AAC "

AAA Lys (K)

AAG "

AGT Ser (S)

AGC "

AGA Arg (R)

AGG "

GTT Val (V)

GTC "

GTA "

GTG "

GCT Ala (A)

GCC "

GCA "

GCG "

GAT Asp (D)

GAC "

GAA Glu (E)

GAG "

GGT Gly (G)

GGC "

GGA "

GGG "