Genome finishing

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	|8-1||8-6||8-3||3-7||7-8||8-2||2-8||8-5||5-8||8-4||4-8||6-7||1-3||1-6		|8-1||8-6||8-3||3-7||7-8||8-2||2-8||8-5||5-8||8-4||4-8||6-7||1-3||1-6
	|-		|-
-	|L||L||L||||L||L||L||L||L||L||L||L||L||?	+	|L||L||L||||L||L||L||L||L||L||L||L||L||L
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	|P||P||A||P||A||A||P||A||P||P||A|| || ||?		|P||P||A||P||A||A||P||A||P||P||A|| || ||?

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Revision as of 02:04, 17 August 2010

Contents 1 PCR 1.1 Arrange Scaffold 1.2 Sequencing 2 Reference

PCR

8-1

8-6

8-3

3-7

7-8

8-2

2-8

8-5

5-8

8-4

4-8

6-7

1-3

1-6

L

L

L

L

L

L

L

L

L

L

L

L

L

P

P

A

P

A

A

P

A

P

P

A

?

• L: 454 PE link
• P: PCR
• A: Assemble

Arrange Scaffold

• Pieces
  • 8-1
  • 8-6
  • 8-3(RC)-7-8
  • 8-2-8
  • 8-5-8
  • 8-4-8

Sequencing

• Primer: Product

1. 5tail-8head: ok
2. 8tail-8head: 4tail-8head
3. 1tail-3head: 7head-3head - 1tail primer의 중간부터 끝 부분이 7 head에 붙은 것으로 생각됨.
4. 7head-3head: ok
5. 5kb control- c1_4-c1_5: ok *gap -> CGTCTAAAAAATTATAATTTTTTAGACG

Reference

• Finishing Overview - PDF
• Consed--A Finishing Package (Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)
• Genomics Education - see some tutorials for finishing with Consed
• Automated Finishing with Autofinish
• Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
• Google Search Result: genome+sequencing+finishing+pcr+protocol