BLAST

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313

Glossary

1˚

The abbreviation for primary. 1˚ sequence

refers to the letters of DNA, RNA, or pro-

tein. 1˚ transcript refers to an unproc-

essed RNA that still contains its introns.

2˚

The abbreviation for secondary. Most fre-

quently used for generalizing protein and

RNA structures; for example, the α-helix

and hair-pin are common 2˚ structures.

3´

The end of a nucleic acid sequence; often

used with UTR.

5´

The start of a nucleic acid (DNA or RNA)

sequence; often used in conjunction with

UTR (e.g., 5´UTR). Nucleotide sequences

are conventionally written with the 5´ end

at the left. DNA molecules are usually

double-stranded but when written, usu-

ally only the 5´ to 3´ strand is displayed.

The complementary strand has reversed

polarity (3´ to 5´).

aa

The abbreviation for an amino acid that is

often used when describing the length of a

protein (e.g., the average protein is about

300 aa long).

allele

A form of a gene. Typically, the most

common form is called wild-type, and

each allele is given a specific (and often

obscure) name.

amino acid

The basic building block for all proteins.

There are 20 common amino acids.

Arabidopsis thaliana

Known by its common name, thale cress,

this mustard weed is a favorite organism

for plant genetics and molecular biology.

It was the first plant with a complete

genomic sequence. For more information,

see http://www.arabidosis.org.

bit

The contraction for binary digit. The

base-2 logarithm of a number is in units of

bits.

BLOSUM

The abbreviation for a blocks substitution

matrix. Matrix names are followed by a

number (e.g., BLOSUM62) that indicate

the minimum percent identity between

any two aligned sequences.

bp

The abbreviation for base pair. The length

of DNA is usually given in bp or nt, Com-

mon measures include Kb, Mb, and Gb

for thousands, millions, and billions of bp,

respectively.

C-terminus

The end of a protein. In text form, the

C-terminus of the protein is always at the

right.

Caenorhabditis elegans

A nematode (also called a roundworm)

that is about 1 mm long and has about

CDS

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314 | Glossary

1,000 cells as an adult. C. elegans was the

first animal to have its complete genome

sequenced. See http://www.wormbase.org.

CDS

The abbreviation for a coding sequence.

CDS isn’t synonymous with exon, since

exons may contain noncoding sequence.

codon

Three contiguous letters of DNA or RNA.

Each of the 64 codons specifies either an

amino acid or a translation stop.

complement

The complement of a DNA sequence is

the sequence on the other strand. For

example, the complement of ACCCGT is

TGGGCA. To complement a sequence in

Perl, use either of the following:

# 4-letter alphabet

$dna =~ tr/ACGT/TGCA/;

# 15-letter alphabet

$dna =~ tr[ACGTRYWSKMBDHV]

[TGCAYRSWMKVHDB];

Drosophila melanogaster

The common fruit fly. This is one of the

most famous organisms for genetic

research and was one of the first animals

whose complete genomic sequence was

determined. See http://www.fruitfly.org.

dynamic programming

A common technique that reduces the

computational complexity of a problem

by finding and extending a partial optimi-

zation.

E. coli

Eschericia coli. A common bacteria nor-

mally found in your gut and a favorite

organism for molecular biology research.

Some variants cause food poisoning.

effective length

Karlin-Altschul statistics assume

sequences of infinite length. To adjust for

edge effects in real sequences, the search

space is reduced by adjusting the true

lengths of the sequences to effective

lengths.

entropy

Randomness; disorder; unpredictability.

eukaryote

Organisms with intracellular membra-

nous organelles such as the nucleus and

mitochondria are called eukaryotes.

frame-shift mutation

A mutation that causes an insertion or

deletion of nucleotides that isn’t a multi-

ple of three, and therefore causes the read-

ing frame to change.

gene

A functional unit of the genome. When

not specifically stated, “gene” is usually

considered a “protein-coding” gene, but

many genes don’t contain the instructions

for proteins (e.g., various RNA genes).

genetic code

The mapping of codons to amino acids.

See Table 2-3.

genetic drift

The tendency of sequences to change over

time by accumulating random mutations.

genome

The complete genetic material for an

organism. For eukaryotes, the genome

refers to the nuclear genome and doesn’t

include organelles.

global alignment

An alignment algorithm that requires

every letter of each sequence to appear in

the alignment. Globally aligning

sequences of different lengths may lead to

very strange alignments.

homologous

In sequence analysis, homologous means

derived from a common ancestor.

Sequences are either homologous or they

aren’t. It is incorrect to say that sequences

are 80 percent homologous unless you

mean that there is an 80 percent chance of

common ancestry. Use percent identity to

describe the similarity of alignments.

hydrophilic

Literally, “likes water.” Water is a polar

molecule that mixes well with other polar

molecules. The charged amino acids K, R,

D, and E, are examples of hydrophilic

amino acids.