E D R , A S I H C RSS

Bioinformatics


1. †Œœ


  • ด๋ฆ„ : Bioinformatics
  • ฐธ—ฌ :  •ฌ๋ก
  • ธฐ„ : 2002. 3. 14 ~ 2002.8.xx
  • ”„๋กœ Šธ ‹œž‘๋™ธฐ™€ ๋ชฉ  : ๋ณธ —ฐตฌ๋Š” ฐจ„ธ๋Œ€ Bioธฐˆ —„œ ปด“จ„ „ณตž๋กœ„œ  ‘•  ˆ˜ žˆ๋Š” ธฐˆ ธ Bioinformatics— ๋Œ€•œ ธฐดˆ๋ฅผ ๋‹ฆ๋Š” ฒƒ„ ๋ชฉ œผ๋กœ •œ‹ค.
  • ”„๋กœ Šธ „–‰ : ตžฌ˜  •๋ฆฌ™€ ด€๋ ›น‚ฌŠธ˜ ๋งฌ, ด€๋ จ ๋ฌธ„œ  •๋ฆฌ๋ฅผ ฃผ•œผ๋กœ •˜ Šต๋‹ˆ๋‹ค. ๋‹ˆœ ๋ฒˆ—ญ๋ณด๋‹ค๋Š” ˜๋ฏธžˆ๋Š” žฌ •๋ฆฌ ณผ •— ๋…ธ๋ „ ธฐšธ˜ˆ •ž…๋‹ˆ๋‹ค.
  • ตžฌ : โ€œBioinformatics: A practical guide to the analysis of genes and proteinsโ€, Second Edition edited by Baxevanis & Ouellette

2. ฑ… •๋ฆฌ


2.1. NCBI DataModel

™œ Model„ šฉ•˜๋Š”ฐ€? ‹ œ— ฐ€นŒšด ๋ชจ๋ธ€ ‹ œ๋กœ –ด๋‚˜๋Š” „ ๋ณด๋‹ค ๋” ž˜ •‹œ‚ค  ˜ˆธกฐ€๋Šฅ•˜ฒŒ •œ‹ค.
ด๋Ÿฐ ง€—„œ NCBI๋Š” sequence-related information— ด€•œ ๋ชจ๋ธ„ ๋งŒ๋“ค—ˆ๋‹ค. ธ๋ฆฌ  ด๋Ÿฐ ๋ชจ๋ธ„ šฉ•„œ Entrez(data retrieval system)๋‚˜ GenBank DB(DNA seq.๋ฅผ  €žฅ•ด๋‘” DB, ๋‘ ฐ€ง€๋Š” œ  „ž —ฐตฌ˜ ‘š”•œ data๋“คด๋‹ค.)™€ ฐ™†Œ”„Šธ›จ–ด๋‚˜ †ต•ฉ DB‹œŠค…œ„ ฐ€๋Šฅ•˜ฒŒ ๋งŒ๋“ค—ˆ๋‹ค.

=== GenBank flatfile & format VS NCBI data model===
GenBank flatfile€ DNA-centered˜ ๋ณด „œด๋‹ค. DNA‘‹ด๋ผ๋Š” ฒƒ€ –ด๋–ค ๋‹จ๋ฐฑงˆ˜ œ  „ž  •๋ณด๋ฅผ  €žฅ•˜  žˆ๋Š” DNA˜—ญด DNAœ„˜ coding regionด๋  ๋ถˆ๋ฆฐ๋‹ค. ๋ฐ˜๋Œ€๋กœ ๋Œ€๋ถ€๋ถ„˜ Protein seq. DB๋“ค€ Protein-centered˜ ด€ ด๋ฉฐ, ด๋Š” ๋‹จ๋ฐฑงˆณผ œ  „ž ‚ฌด๋Š” accesion number(œ  „ž๋ฅผ  ‘•˜ธฐœ„•œ DB˜ keyฐ’) ... „–‰‘

3. šฉ–ด ฐธกฐ

3.1. NCBI ๋ž€

National Center for Biotechnology Information ๋ถ„ž ƒ๋ฌผ  •๋ณด๋ฅผ ๋‹ค๋ฃจ๋Š” ตญฐ€ ž๋ฃŒ›œผ๋กœ„œ „ค๋ฆฝ๋˜—ˆœผ๋ฉฐ, NCBI๋Š” ณตšฉ DB๋ฅผ ๋งŒ๋“ค๋ฉฐ, „‚ฐ— ด€•œ ƒ๋ฌผ•™— —ฐตฌ๋ฅผ ด๋Œ  žˆœผ๋ฉฐ, Genome ž๋ฃŒ๋ฅผ ๋ถ„„•˜ธฐ œ„•œ software ๋„ตฌ๋ฅผ œ๋ฐœ•˜ , ƒ๋ฌผ•™  •๋ณด๋ฅผ ๋ณดธ‰•˜  žˆŠต๋‹ˆ๋‹ค. - ฆ‰, „˜ ฑด•ณผ งˆ๋ณ‘— ˜–ฅ„ ๋ฏธ˜๋Š” ๋ฏธ„•œ ณผ •๋“ค„ ๋ณด๋‹ค ๋” ž˜ ••˜ธฐ œ„•œ ๋ชจ๋“  ™œ๋™„ ˆ˜–‰

Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

3.2. Entrez ๋ž€

Entrez๋Š” †ต•ฉ ๋ฐ„ฐ๋ฒ Šค retrieval ‹œŠค…œœผ๋กœ„œ DNA, Protein, genome mapping, population set, Protein structure, ๋ฌธ—Œ ฒ€ƒ‰ฐ€๋Šฅ•˜‹ค. Entrez—„œ Sequence, Šนžˆ Protein Sequence๋Š” GenBank protein translation, PIR, PDB, RefSeq๋ฅผ ฌ••œ‹–‘•œ DB๋“ค— žˆ๋Š” „œ—ด„ ฒ€ƒ‰•  ˆ˜ žˆ๋‹ค.
...„–‰‘

4. ƒ๋ฌผ•™ธฐดˆ

4.1. ๋‰ดด๋ ˆ˜‹ฐ๋“œ(nucleotide)๋ž€

DNA™€ RNA๋ฅผ ตฌ„•˜๋Š” nucleotide๋Š” ‚ฐธฐ(Phophate), 5 ƒ„‹น(Sugar)ธ ๋””˜‹œ๋กœ๋ณดŠค(deoxyribose), 4 ข…๋ฅ˜˜ งˆ†Œ —ผธฐ(Base) ‘ •˜๋‚˜๋ฅผ ฌ••˜—ฌ 3œ˜ ๋ถ€œ„(Phophate, Sugar, Base)๋กœ ตฌ„ฑ๋œ ๋ฌผงˆด๋‹ค. ๋‹€ ‚ฐณผ —ผธฐ๋ฅผ —ฐฒฐ‹œ‚จ๋‹ค. (šฉ–ด„ค๋ช…. ‘•ฉ : ๋งŽ€ ๋ถ„žฐ€ ฒฐ••˜—ฌ ฐ ๋ถ„ž๋Ÿ‰˜ ™”•ฉ๋ฌผ๋กœ ๋˜๋Š” ๋ณ€™”)
‚ฐธฐ๋Š” ATP—(œ€ ด ATP๋ฅผ †Œ๋น„•„œ —๋„ˆง€๋ฅผ ๋‚ธ๋‹ค. ข…˜ —๋„ˆง€›.) žˆ๋Š” ž˜ •Œ๋ „ ‚ฐ„ธฐด๋‹ค. DNA ๋ถ„ž๋ฅผ ตฌ„• •Œ—๋Š” ๋‹— ง ‘ —ฐฒฐ๋œ •˜๋‚˜˜ ‚ฐธฐ๋งŒ ๋‚จ๋Š”๋‹ค. 5 ƒ„‹น ๋””˜‹œ๋กœ๋ณดŠค(deoxyribose)๋Š” ATP˜ 5 ƒ„‹น ๋ฆฌ๋ณดŠค(ribose)™€ ๋งคšฐ œ ‚ฌ•˜‹ค. deoxyribose๋Š” ribose˜ 2๋ฒˆ ƒ„†Œ— žˆ๋Š” -OH ธฐ ๋Œ€‹  -Hธฐ๋ฅผ ฐ€ง€  žˆ๋‹ค. deoxyribose˜ 5œ ƒ„†Œ—๋Š” 1๋ฒˆ—„œ 5๋ฒˆนŒง€ ˆซžฐ€ ๋ถ™—ฌ„‹ค.

DNA— กดžฌ•˜๋Š” 4ข…๋ฅ˜˜ —ผธฐ๋Š” •„๋ฐ๋‹Œ(adenine), ตฌ•„‹Œ(guanine), ‹ฐ๋ฏผ(thymine), ‹œ† ‹ (cytosine), šฐ๋‹ค(uracil)ด๋‹ค. ด๋“ค ‘—„œ ”ผ๋ฆฌ๋ฏธ๋”˜(pyrimidine)ด๋  ๋ถ€๋ฅด๋Š” thymine, cytosine, uracil€ งˆ†Œ™€ ƒ„†Œ๋กœ ตฌ„ฑ๋œ 6ฐ˜•˜  ๋ฆฌ๋กœ ๋˜–ด žˆ๋‹ค. “จ๋ฆฐ(purine)ด๋  ๋ถ€๋ฅด๋Š” adenine, guanine€ ๋” ๋ณตžก•˜—ฌ, งˆ†Œ™€ ƒ„†Œ๋กœ ตฌ„ฑ๋œ 6ฐ˜•ณผ 5ฐ˜•˜ ‘  ๋ฆฌ๋กœ ด๋ฃจ–ด„‹ค. nucleotide—„œ ด๋“ค —ผธฐ๋“ค€ deoxyribose˜ 1๋ฒˆ ƒ„†Œ— ณตœ ฒฐ•œผ๋กœ —ฐฒฐ๋˜–ด žˆœผ๋ฉฐ, ‚ฐธฐ๋Š” 5๋ฒˆ ƒ„†Œ— —ญ‹œ ณตœ ฒฐ•œผ๋กœ —ฐฒฐ๋˜–ด žˆ๋‹ค. adenine, guanine, cytosine, thymine, uracil€ ฐฐ A, G, C, T,U ๋กœ ‘œธฐ๋œ‹ค.<ธ๋ฆผ 1>

4.2. DNA VS RNA

•‚ฐ(Nucleic acid)๋ถ„ž๋Š” ๋ฏฟ„ ˆ˜ —†„  •๋„๋กœ ธด ‘•ฒดด๋ฉฐ, ฐ ๋ถ„ž๋Š” ตฌกฐ ๋‹œ„ธ nucleotide๋ฅผ ˆ˜๋ฐฑ๋งŒ œ”ฉ ฌ••˜  žˆ๋‹ค.
Nucleic acid๋Š” base˜ ข…๋ฅ˜™€ 5-carbon sugar˜ ข…๋ฅ˜, ๋ถ„ž ตฌกฐ— ๋”ฐ๋ผ DNA™€ RNA๋กœ ๋ถ„๋ฅ˜๋œ‹ค.
•‚ฐ—ผธฐ˜ ข…๋ฅ˜5„ด๋‹˜ ข…๋ฅ˜๋ถ„ž ตฌกฐ
DNAA, G, C, TDioxyribose2‘ ๋‚˜„ 
RNAA, G, C, URibose‹‚ฌŠฌ

4.3. DNA

ธ๋ฆผ€ DNA˜ ๋ชจ‹๋„ด๋‹ค.
DNA๋Š” a twisted ladder๋  ‘œ˜„๋˜๋Š”๋ฐ ‚ฌ๋‹ค๋ฆฌ˜ ฐฐ˜ strand๋Š” ๋‹ณผ ‚ฐ˜ ฒฐ•„ ˜๋ฏธ•˜ , lung€ Base๋“ค˜ ฒฐ•„ ˜๋ฏธ•œ‹ค. Base๋“ค€ ‚ฌ˜ ฒฐ•€ ˆ˜†Œฒฐ•„ ด๋ฃจ๋Š”๋ฐ, A™€ T, C™€ Gฐ€ ฒฐ•ด๋ฃจ–ด„‹ค. ๋”ฐ๋„œ DNA๋ฅผ ๋ถ„„•ด base๋“ค˜ ˆ˜๋ฅผ ๋น„ต•ด๋ณด๋ฉด A™€ T˜ ˆ˜ฐ€ ฐ™ , C™€ G˜ ˆ˜ฐ€ ฐ™Œ„ •Œ ˆ˜ žˆ๋‹ค. — •œชฝ ฐ€๋‹— žˆ๋Š” nucleotide๋Š” ๋‹ค๋ฅธชฝ ฐ€๋‹˜ nucleotide „œ—ด„ ฒฐ ••˜ฒŒ ๋œ‹ค. ธ๋ž˜„œ ธ ๋‘ ฐ€๋‹„ ƒ๋ณด  (complementary) ด๋  •œ‹ค. ฆ‰, DNA ๋ถ„ž๋ฅผ ˆ˜งœผ๋กœ ธ๋ฆฌ๋ฉด •œ ฐ€๋‹€ 5'—„œ 3'œผ๋กœ œ„—„œ •„๋ž˜๋กœ‹ฌ๋ฆฌ , ๋‹ค๋ฅธ ฐ€๋‹€ 5'—„œ 3'œผ๋กœ •„๋ž˜๋กœ œ„๋กœ‹ฌ๋ฆฐ๋‹ค.(5', 3' šจ†Œ๋  •Œ  žˆŒ,  •™•žŒ ๋ชจ๋ฆ„)

4.4. DNA Republication

™“Šจณผ ฌ๋ฆญ€ DNA˜ ตฌกฐ, Šนžˆ Œ„ ด๋ฃฌ nucleotide˜ ƒ๋ณด„œ  „๋ฌผงˆ˜  •™••œ ๋ณต œธฐž‘˜ •‹ž„„ •Œ•˜‹ค. ธ๋“ค€ "šฐ๋ฆฌฐ€ ฐ€ ••œ —ผธฐŒ ˜•„›๋ฆฌฐ€ œ  „ ๋ฌผงˆ˜ ๋ณตธฐž‘„  œ‹œ•˜  žˆŒ„ ๋А๋‚„ ˆ˜ —ˆ๋‹ค."๋  ๋ง•˜˜€๋‹ค. ธ๋“ค€ ‘ ๋‚˜„ ˜‘ ฐ€๋‹ด ๋ถ„๋ฆฌ๋˜  ฐฐ˜ ฐ€๋‹„ ฃผ˜• (template)œผ๋กœ •˜—ฌ ƒˆ๋กœšด ƒ๋ณด  ‚ฌŠฌ˜•„ฑ๋œ‹ค๋Š” ๋‹ˆœ•œ ๋ณต œ๋ชจ๋ธ„ ๋งŒ๋“ค—ˆ๋‹ค.

4.5. DNA˜ —ผƒ‰ฒด๋‚ด—„œ˜ Žธ„ฑ(Organization)

„˜ —ผƒ‰ฒด(chromosome)˜ ข…๋ฅ˜๋Š” 23œด๋‹ค. 22œ๋Š” ƒ—ผƒ‰ฒด(autosome)  1œ๋Š” „—ผƒ‰ฒด(sex chromosome)ด๋‹ค. •œ ข…๋ฅ˜˜ —ผƒ‰ฒด๋Š” „œ๋กœ˜ Œ„ ฐ€ง€  žˆ๋‹ค. ๋”ฐ๋„œ „˜ —ผƒ‰ฒดตฐ(genome)€ 46œ˜ chromosomeœผ๋กœ ตฌ„ฑ๋˜–ด žˆ๋‹ค. chromosome€ „ฌ๋‚ด—„œ ๋Œ€๋ถ€๋ถ„˜ ‹œ„„ ‹ƒ€๋ž˜(fiber)ฐ™€ ˜•ƒœ๋กœ žˆ๋Š”๋ฐ.. ด๋Š” chromosome ธฐ๋ณธ๋‹œ„ธ ๋‰ดด๋ ˆ˜†œ(Nucleosome)๋“คฒฐ•ฉ๋œ ˜•ƒœด๋‹ค. ด nucleosome€ •˜๋‚˜˜ žˆŠค†ค(histone)๋‹จ๋ฐฑงˆ„ DNAฐ€ ๋‘๋ฒˆ œ˜ฐ€ ˜•ƒœด๋‹ค. --ž‘„‘

4.6. Gene๋ž€

œ  „ ˜•งˆ„ ๋ง•˜๋ฉฐ œ  „— ด€—ฌ•˜๋Š” Šน • ๋ฌผงˆด๋‹ค. Gene˜ ๋ชจž„ด Genomeด๋‹ค. ๋˜•œ ด Gene๋Š” DNA— ธ ๋‚ดšฉ•”˜™” ๋˜–ด žˆ๋‹ค. ด๋ฏธ •Œ  žˆ„ง€๋„ ๋ชจ๋ฅด ง€๋งŒ, Geneด๋ผ๋Š” ฒƒ€ DNA˜ —ผธฐ ๋ฐฐ—ดด๋‹ค. —ผธฐ ๋ฐฐ—ด(base sequence)–ด๋–ค ณผ •„ †ต•„œ ๋Œ€‘๋˜๋Š” ˆœ„œ๋กœ •„๋ฏธ๋…ธ‚ฐ(amino acid)๋ผ๋ฆฌ˜ peptideฒฐ•„ •˜—ฌ ๋‹จ๋ฐฑงˆ๋กœ ๋‚˜ƒ€๋Š” ฒƒ„ œ  „ ˜•งˆ ๋ฐœ˜„ด๋  •œ‹ค.
šฐ„  ƒ๋ฌผ•™˜ •‹ด๋ก ด Central Dogma(‘‹ด๋ก )— ๋Œ€••Œ•„๋ณด ‹ค.
ด๋ก € DNAฐ€ –ด๋–ปฒŒ ๋‹จ๋ฐฑงˆ„ ƒ„•˜๋Š” ฐ€๋ฅผ ๋ณด—ฌฃผ  žˆ๋‹ค.
๋ฆผ. 1
ธ๋ฆผ 1„ ฐธกฐ•˜๋ฉด DNA๋Š” 2‘ ๋‚˜„ ˜• ตฌกฐ๋กœ ๋˜–ดžˆ๋‹ค. ฒƒ„ฌ ๋ถ„—ด ณผ •—„œ DNA— œ  „•”˜ธ๋ฅผ ๋ณต‚ฌ•œ mRNA๋กœ ๋ฐ”๋€Œ๋ฉฐ ด mRNAฐ€ Ribosome— ๋“ค–ดฐ€๋ฉด tRNA๋Š” mRNA— ๋‹ฒจžˆ๋Š” DNAœ  „•”˜ธ๋ฅผ ๋ถ„„•˜—ฌ„œ ๋Œ€‘๋˜๋Š” amino acid๋ฅผ ฐ€ ˜จ๋‹ค. ด๋Ÿฐ ณผ •ด ๋ฐ˜๋ณต๋˜ , amino acid‚ฌ—๋Š” peptideฒฐ•„ ด๋ฃจ๋ฉด„œ ด๋Š” ๋‹จ๋ฐฑงˆ๋กœ ˜•งˆ ๋ฐœ˜„ด ๋œ‹ค. -- „–‰‘..

Bioinformatics๋ฅผ ณต๋ถ€•˜ ค๋Š” ‚ฌ๋žŒ๋“ค„ œ„•

 ˆ๋Œ€ ปด“จ„ง€‹๋งŒœผ๋กœ Šน๋ถ€ฑธ๋   •˜ง€ ๋ง•„••  ฒƒ ž…๋‹ˆ๋‹ค. ปด“จ„ง€‹๋งŒœผ๋กœ๋Š”  •๋ง ธฐˆ ž ˆ˜ค€ ๋ฐ–— ๋˜ง€ ๋ชป•ฉ๋‹ˆ๋‹ค. ชฝ ง€‹•„š”•˜‹  •ด๋„ ฑด ธฐˆ   ง€‹ด๋ธฐ๋ณด๋‹ค๋Š” ณผ•™, ฆ‰,  „‚ฐ•™(Computer Science)˜ ง€‹•„š”•ฉ๋‹ˆ๋‹ค. ธ๋ฆฌ  Bioinformatics๋ฅผ  œ๋Œ€๋กœ ณต๋ถ€•˜ ค๋ฉด ปด“จ„ฐ ๋ถ„•ผ๋ฅผ ๋นผ ๋„ œ†Œ•œ ƒ๋ฌผ•™ œ๋ก , ๋ถ„ž ƒ๋ฌผ•™, ƒ™”•™, œ  „•™, †ต„•™ œ๋ก , ™•๋ฅ ๋ก , ๋‹ค๋ณ€๋Ÿ‰ †ต„•™, ๋ฏธ ๋ถ„„ •Œ•„••ฉ๋‹ˆ๋‹ค. ด๋Ÿฐ ฒƒ„ ๋ชจ๋ฅด  ๋›ฐ–ด๋“คฒŒ ๋˜๋ฉด ฐ€žฅž๋ฆฌ๋งŒ ๋งด๋ŒฒŒ ๋ฉ๋‹ˆ๋‹ค. ตญ๋‚ด—„œ Bioinformatics๋ฅผ •˜ ค๋Š” ๋Œ€๋ถ€๋ถ„˜  „‚ฐ•™ณผ ตˆ˜‹˜๋“คด ๋ถ€๋ฅ˜— †•œ‹ค๋Š”  „œธ€”ˆ ‚ฌ‹ .

 œ๋Œ€๋กœ ๋œ •ˆ๋‚ด๋ฅผ ๋ฐ›œผ๋ ค๋ฉด, ›„—ฐ ๋ฐ•‚ฌ๋‹˜˜ ‚ฌŠธ๋ฅผ ถ”œ•ฉ๋‹ˆ๋‹ค. http://www.bioinformatics.pe.kr/ -- น€ฐฝค€

DeleteMe QnA๋ฅผ –ด ๋ณด•˜๋Š”๋ฐ ž‹ ฐด '๋š' ๋–จ–ดง€๋Š”ตฐš”.(ฒƒ๋งŒ•„‹ˆ–ด๋‘ ˜ค๋Š˜ ตžฌ๋ฅผ ๋ณด๋Š”๋ฐ ˜Œ๋ณด๋Š” ƒ†Œ•œ‹–ด๋“ค ๋•Œ๋ฌธ— ‚ฌ „ ฐพœผ๋žด, ‚ฌŠธ ๋Œ•„‹ค๋‹ˆ๋ฉฐ –ด๋–ค ฑดง€ •Œ•„๋ณด๋žด, •ด๋งธ๋Š”๋ฐ..) ธ๋ž˜‘, ด๋ฆ„„ „ธ๋ฒˆด๋‚˜ ‹€๋ฆฐ •™๋ฌธด ๋ญ”ง€๋Š” •Œ  ‹ ,:) ๋‹Œ— ˜‹œ  €™€ ๋น„Š•œ ง€‹๋งŒ ฐ€„ ‚ฌ๋žŒชฝ— ด€‹„ ฐ€ง€  —ฐตฌ๋ฅผ • •Œ ๋„›€ด ๋  ˆ˜ žˆ—ˆœผ๋ฉด •ฉ๋‹ˆ๋‹ค.

DeleteMe –ด„œ ”„๋กœ Šธ๋•  •๋„˜ „ณผ๋ฅผ ๋งŒ๋“ค–ด• ตฐš”.

Valid XHTML 1.0! Valid CSS! powered by MoniWiki
last modified 2021-02-07 05:22:36
Processing time 0.0319 sec