数据处理光谱分析与数据挖掘

Center Star for Multiple Sequence Alignment
input sequences
trie trees
… search
final result
sum up
update
From Trie to Suffix Tree
Trie
S1=AGACGT S2=AGCCTA S3=GCAGCC S4=CGTACT
S7=
… AGCCTAGCAGCCCGTACT
Greedy search with suffix tree
S=GTCCGAAGCTCCGG
T=GTCCTGAAGCTCCGT 1234567890123456
(1,1,4) (5,6,9)
Extreme MSA for Very Similar DNA Sequences
– BLAST: Basic Local Alignment Search Tool
Query
Database
Output
Multiple Sequence Alignment(MSA): What & Where
input
Output
Multiple Sequence Alignment(MSA): What & Where
• Global alignable
– pairwise – multiple
• Prove
– optimization
Global alignable
Extreme center star
MapReduce for Center Star Frame
input fasta file
local file system
Multiple Sequence Alignment(MSA): What & Where
• Different from Mapping, Assembly, BLAST
Multiple Sequence Alignment(MSA): What & Where
• Different from Mapping, Assembly, BLAST
Multiple Sequence Alignment
Phylogenetic tree
Multiple DNA Sequence Alignment
Multiple Similar DNA Sequence Alignment
Our Focus
Virus sequences
Population SNV calling
sum up
update
How to set k for k-band?
Detecting the matching region with Trie
S=AGACGTAGCCTAGCAGCCCGTACT
S1=AGACGT S2=AGCCTA S3=GCAGCC S4=CGTACT
T=AGACCTAGCTAGCAGCCCGTACACT
… Application
Techniques for similar DNA MSA
j
0
1
2
i
c
a
K-band
0
0
-1
1a
-1 -1
1
2c
-2
1
0
3g
0
0
4c
-1
5t
6g
1. k-band Dynamic Programming
3
4
5
t
g
t
-4
-5
0
-1
0
-1
-1
2
-1
1
1
1
0
3
3
2
Techniques for similar DNA MSA
input sequences
… search
final result
sum up
update
Experiments
• 100 human mitochondria genome sequences • 16k length (1555KB)
Running time
Center Star
12933.2s
Suffix Tree
S1=AGACGTAGCCTAGCAGCCCGTACT
S2= GACGTAGCCTAGCAGCCCGTACT
S3= ACGTAGCCTAGCAGCCCGTACT
S4= CGTAGCCTAGCAGCCCGTACT
S5=
GTAGCCTAGCAGCCCGTACT
S6=
TAGCCTAGCAGCCCGTACT
2. Center star strategy
Baidu Nhomakorabea
S1
S3
S2
S4
S5
tree alignment
S1
S3
S5
S2
S4
Center star strategy
Center Star for Multiple Sequence Alignment
input sequences
… search
final result
HDFS
Software
http://datamining.xmu.edu.cn/software/halign/ http://lab.malab.cn/soft/halign/
Quan Zou, Qinghua Hu, Maozu Guo, Guohua Wang. HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy. Bioinformatics. 2015,31(15): 2475-2481
Suffix tree Trie
center center
star
star
24.8s
15.6s
K-band center star
10.9s
Extreme Extreme
Trie
suffix tree
19.7s
5.4s
• Our output 1558KB • ClustalΩ 1627KB
Discuss: How to measure the similarity?