바이오인포메틱스 —기본개념들

Jay

·

Follow

2 min read

·

Feb 24, 2019

--

Listen

Share

1. 기본개념들

1.1 종류

A   Adenine
C   Cytosine
G   Guanine
T   Thymine

1.2 페어

G-C | C-G
A-T | T-A

• ACGT 이외의 알파벳이 나타내는 의미

Y     Pyrimidine (C or T) 
R     Purine (A or G) 
W     Weak (A or T)
S     Strong (G or C) 
K     Keto (T or G) 
M     Amino (C or A)     
D     A, G, T (not C - remember as after C)
V     A, C, G (not T - remember as after T/U - We'll get to "U" soon) 
H     A, C, T (not G - remember as after G)
B     C, G, T (not A - remember as after A)
N     Any base
-     Gap

Certain groups of nucleotides that share some common attribute may be designated by so called ambiguity codes — biostar handbook

1.3 Genome

• coding region vs junk region, (controversy : C Value Paradox)
• sizes:

Ebola virus genome: 18 thousand basepairs (18Kb)
E.coli bacteria genome: 4 million basepairs (4Mb)
Baker's yeast fungus genome: 12 million basepairs (12Mb)
Fruit fly genome: 120 million basepairs (120Mb)
Human genome: 3 billion basepairs (3Gb)
Some salamander species: 120 billion basepairs (120 Gb)

1.4 RNA

• T (Thymine) is replaced by the nucleotide U (Uracil)
• 따라서 ACGU

T --> U

• mRNA, tRNA, rRNA, etc

1.5 Protein

• 20종류

ARNDCEQGHILKMFPSTWYZ

• DNA → mRNA → Protein
• Translation table (아래는 예시)

CGU, CGC, CGA, CGG, AGA, AGG --> Arginine (Arg/R)

1.6 ORF

• open reading frame(at least, say, 100 consecutive codons without a stop
  codon)

1.7 Gene

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and other functional sequence regions.

1.8 Other region

1. UTR(Untranslated regions)
2. Promoter regions
3. CpG islands
4. Enhancers

1.9 Homology

• Two regions of DNA that evolved from the same sequence

Homology is not a synonym of sequence similarity!
Homologous sequences are usually similar to one another, but similarity of sequences does not indicate homology.