rna sequence assembly
DESCRIPTION
RNA Sequence Assembly. WEI Xueliang. Overview. Sequence Assembly Current Method My Method RNA Assembly To Do. Sequence Assembly. Goal : get the DNA/RNA sequence. Machine cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases. Define: Read = Tag = Fragment. - PowerPoint PPT PresentationTRANSCRIPT
RNA Sequence Assembly
WEI Xueliang
Overview
• Sequence Assembly• Current Method• My Method• RNA Assembly• To Do
Sequence Assembly
• Goal : get the DNA/RNA sequence.
• Machine cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases.
• Define: Read = Tag = Fragment
De novo sequence assembly
Overview
• Sequence Assembly• Current Method• My Method• RNA Assembly• To Do
De novo sequence assembly
Calculating the overlap need huge amount of time.
DE BRUIJN GRAPH
K-Mer : Length k substring of the Tag.
Each nodes only have 4 out degrees at most.
Hashing the node. “CTG”=>(132)4=(30)10
“CTG”=>”TGG” (132=)4 shift left. (1320)4 module (1000)4
(320)4 + (3)4 ‘G’ (323)4
DE BRUIJN GRAPH (CONT’)
If there are repeats, like ”GACT”
3-Mer De Bruijn can not know which way is the correct way. 6-Mer can get the correct sequence.
Larger K, better result.
De novo sequence assembly
Suppose use K = Length of Tag. (20-Mer) TGACGTAGCTATGTATTTTG GACGTAGCTATGTATTTTGT (no 20-Mer)
Coverage is not enough to support large K.
Overview
• Sequence Assembly• Current Method• My Method• RNA Assembly• To Do
MY METHOD.
Tag length=6, K=3 When we have
AAGACT? Try all the way:
AAGACTC AAGACTT AAGACTG
Check Tag : AGACTC
The correct way should be AAGACTC
Overview
• Sequence Assembly• Current Method• My Method• RNA Assembly• To Do
RNA ASSEMBLY
ALTERNATIVE SPLICING
The graph
All cDNA sequences.
RNA ASSEMBLY’S PROBLEM
Merge? Index the sequence.
RNA ASSEMBLY’S PROBLEM(CONT’)
Solution?
RNA ASSEMBLY’S PROBLEM(CONT’)
Index Tags
RNA ASSEMBLY’S PROBLEM(CONT’)
Solution?
Speed?
SINGLE TAG’S LIMITATION
|Yellow Sequence| >= Length of Tag Length of Tag 25-100bp. Single Tag is not enough!
DATASET - PAIRED END TAGS
Fragment length usually > 1k Some RNA sequence is shorter than 1k.
TO DO
Handle large data-sets. (10G) Improve accuracy. Using PETs data.
Thanks!!