数据库使用 杨建华 2010/9/28

Outline of the Topics UCSC and Ensembl Genome Browser (Blat vs Blast vs Blastz vs Multiz) 挖掘数据用 Table Browser 或 BioMart 用户友好化你的数据 写自动查询程序 基因组浏览器的介绍 序列查询

UCSC Genome Browser Introduction Jim Kent (

Organization of genomic data… Genome backbone: base position number Annotation Tracks chromosome band known genes predicted genes evolutionary conservation SNPs sts sites gap locations repeated regions microarray/expression data more… Links out to more data

Ensembl Genome Browser Introduction Ewan Birney

1 1 Select Clade 2 2 Select Species 3 3 Select Assembly 4 4 Position or Term 5 5 Image width 6 6 Configure track and Image 7 Submit 7 Genome Browser

Protein gene microRNA/snoRNA Multiz Alignment Conserved Score Get ImageGet sequence Genome Browser

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Track colors may have meaning—for example, UCSC Gene track: exon 3’ UTR 5’ UTR Intron, and direction of transcription >> Genome Browser

Phenotype and Disease Mapping and sequencing Gene and Gene Prediction mRNA and ESTExpression and RegulationComparative Genomics Variation and Repeats Genome Browser

Hide: removes a track from view Dense: the track is displayed with all features collapsed into a single line. Squish: the track is displayed with each annotation feature shown separately, but at 50% the height of full mode. Pack: the track is displayed with each annotation feature shown separately and labeled, but not necessarily displayed on a separate line. Full: the track is displayed with each annotation feature on a separate line.

Host Gene of ncRNA and Expression Pattern Example: has-miR-1-1/ has-miR133a-2 and Its Target Gene (Hand2) 1 2

Host Gene of ncRNA and Expression Pattern select

Host Gene of ncRNA and Expression Pattern

select

Host Gene of ncRNA and Expression Pattern

1 2

Blat vs Blast vs Blastz vs Multiz BLAT = BLAST-like Alignment Tool Rapid searches by INDEXING the entire genome Works best with high similarity matches –Kent, WJ. Genome Res :656 Choices Paste one or more sequences

Blastz Alignments

Chain and Net alignment Evolution's cauldron: duplication, deletion, and rearrangement

CTAGGAAAAAATATCTTCATATACTTGTCTGATTATTTCTTTAA GATTCATAAAAGTGG |||||||||||||||||||||||||||||||||||||||||| CTAGGAAAAAATATCTTCATATACTTGTCTGATTATTTCTTT AAAAAAAAAAAAAAGATTCATAAAAGTGAAACAAAGGT ACGATTTTATGT |||||||.|||||||||||||||||||.|||||||||| AAGATTCgTAAAAGTGAAACAAAGGTAtGATTTTATGT snoRNA + intron RetroGene derived from H/ACA snoRNA Evolution's cauldron: duplication, deletion, and rearrangement

Tools -Convert

Tools -LiftOver

Tools -liftOver Paste Data

Tools -liftOver

Track TypeAnnotation Track SQL Table Restricts the query Combines the output of two queries The Table Browser

1. Extract Intron of Protein-coding Gene In the Human Genome 2. snoRNA/microRNA Intersect with Intron Find snoRNA/microRNA located within Intron in the human genome

1 Choose Human genome 2 Choose SQL Table 3 Choose Region 4 Choose Filter Extract Intron of KnownGene In the Human Genome

Output KnownGene as Custom Track

Custom Track Displaying Custom Track in the Browser

Choose SQL Table Intersect with snoRNA/microRNA

summary snoRNA/microRNA Summary Statistics

1.Format the data 2. upload the data 3. display the results in the Genome Browser Displaying liftOver Results in the Chimp Genome

Displaying Results in the Genome Browser

Displaying liftOver Results in the Genome Browser Paste data

Displaying liftOver Results in the Genome Browser

Tools -LiftOver

Writing automated procedures for genome-wide queries Local Browser Installation (Rice UCSC Genome Browser Using the Browser Source Code Base, And so on) Writing a Perl/C/PHP program to automatically extract database data

Thank You ！