Genome finishing

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Revision as of 03:35, 16 August 2010 (view source) Csbl (Talk | contribs) (→Sequencing) ← Older edit		Revision as of 01:30, 17 August 2010 (view source) Csbl (Talk | contribs) (→PCR) Newer edit →
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	==PCR==		==PCR==
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		+	{| class="wikitable" style="text-align:center" border="1"
		+	|+
		+	|8-1||8-6||8-3||3-7||7-8||8-2||2-8||8-5||5-8||8-4||4-8
		+	|-
		+	|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===		===Arrange Scaffold===
	*Pieces		*Pieces

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Revision as of 01:30, 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
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