基因组和转录组高通量测序数据分析流程和分析平台

Comparative genomics --- LCB
Genome A: Genome B:
0
1Baidu Nhomakorabea
2
3 1
4 6
5
6
7
8 5
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 2 7 9 -10 -12 11 14 16 15 17 20 22 -24 21 23 25 8
126_113 G_G 255 A_G
SNP visualization
Genome overview
Features Data Assembly Size(Mb) 37.5 Scaffold N50 (kb) 178 Coverage(fold) 78 G+C content (%) 46.01 GC Exonic (%) 51.73 GC Intronic (%) 47.05 Repeat rate(%) 1.68 Protein-coding genes 9405 Gene density (per Mbp) 250.8 Exons per genes 2.53 tRNAs 72 rRNAs 19 SM(Secondary 28 Metabolism)genes TE 15%
NGS Genomics data NC AN AF MO MAA MAC AO … Meta
Transcriptomics Proteomics Metabonomics
genomics
2. Comparative biology
基因组/转录组 分析流程
质控（QC） 组装（Assembly） 基因预测（Gene prediction） 基因组特征（Genome feature）
m mm fu as ta re ne Score a c r 0 0 0 0 0 0 2 0 0 0 0 -10 0 0 0 0 0 0 2 0 0 0 0 3 0 0 0 0 0 3 0 0 3 0 1 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 3 0 0 3 0 0 0 0 0 0 0 2 0 0 2 0 1 0 0 0 1 0 3 0 1 1 0 0 0 0 0 0 0 2 0 0 3 0 -10 -5.9 -5.6 -4.5 -4.5 -3.7 -3.4
0 -18 -19
3 -4 13
Locally Collinear Blocks (LCBs)
Orthologous gene visualization
Conserved region in an ortholog family
ortholog link between two species
Comparative biology in functional view
178_49 2.21E-12 76 58 95_88 2.48E-51 2.17E-14 4.97E-41
|CDS|O orf19. RF| 6115
|ORF|int orf19. ron| 57 |long_ter gamm + minal a-1a
13717 105673 G_T 13728 105121 A_A
Gene prediction result assessment
DEG & enrichment
Phylogeny tree & evolution time
Comparative genomics --- Dot Plot
translocation
inverted repeats
高通量测序数据（NGS） 数据分析平台
NGS Data Analysis Strategy
Wet lab Database Homology Feature Variation
3. System biology
1. Functional biology
Bio-function Annotation Assembly
基因功能（Gene function）
差异表达分析和富集分析（DEG & enrichment） 同源基因（Homology gene）
系统发育树和进化（ Phylogeny tree & evolution ）
比较基因组学（ Comparative genomics ）
Sequencing quality control
0 0 0 1 0 1 3 0 0 3 0
0 0 0 0 1 0 2 0 0 3 0
-3.1
-2.7
SNP/mutation identification
Alignment based SNP identification and Fisher’s Exact Test:
ID 13 14 17 18 126 Positio Allea n target 954 963 1129 1144 4061 A_A T_C T_G T_C C_G Quality target 31 29_8 29_2 27_31 32_31 30_30 31 Freq target 8 90_1 92_1 171_1 111_2 Allea Quality Freq referenc referenc referenc P-value e e e G_G C_C T_G T_C G_G 31 31 30_27 27_30 32 29 31_32 141 147 78_54 2.01E-13 4.87E-66 4.12E-14 Chromos Annotat Str Gene ome ion and Chr1 Chr1 Chr1 Chr1 Chr1 Chr1 Chr2 |ORF| |ORF| |ORF| |ORF| orf19. + 6115 orf19. + 6115 orf19. + 6115 orf19. + 6115
DB_Desc ve us sa
Database Gene Ontology (GO) Funcat KEGG KOG/COG IPRSCAN Protein family PKS/NRPS Others
SUBFAMILY NOT NAMED Flavodoxin, conserved site Salmonella virulence plasmid 65kDa B protein SpvB Chromo domain subgroup Myelin P0 protein Insecticide toxin TcdB middle/N-terminal Integrin alpha betapropellor PUTATIVE UNCHARACTERIZED PROTEIN Rhs repeat-associated core