数据库使用 杨建华 2010/9/28. outline of the topics ucsc and ensembl genome browser (blat vs...

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

(http://www.genome.ucsc.edu/)

Organization of genomic data…

Genome backbone: base position number

Ann

otat

ion

Tra

cks

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 Introductionhttp://www.ensembl.org

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 exon exon3’ UTR 5’ UTR

Intron, and direction of transcription <<< or >>>

Genome Browser

Phenotype and Disease

Mapping and sequencing

Gene and Gene Prediction

mRNA and EST

Expression and Regulation

Comparative Genomics

Variation and Repeats

Genome Browser

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 PatternExample: 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

Host Gene of ncRNA and Expression Pattern

select

Host Gene of ncRNA and Expression Pattern

Host Gene of ncRNA and Expression Pattern

Host Gene of ncRNA and Expression Pattern

1 2

Host Gene of ncRNA and Expression Pattern

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. 2002. 12:656

Choices

Paste one or more sequences

Blastz Alignments

Chain and Net alignment

Evolution's cauldron: duplication, deletion, and rearrangement

CTAGGAAAAAATATCTTCATATACTTGTCTGATTATTTCTTTAAGATTCATAAAAGTGG |||||||||||||||||||||||||||||||||||||||||| CTAGGAAAAAATATCTTCATATACTTGTCTGATTATTTCTTT-----------------

AAAAAAAAAAAAAAGATTCATAAAAGTGAAACAAAGGTACGATTTTATGT |||||||.|||||||||||||||||||.|||||||||| ------------AAGATTCgTAAAAGTGAAACAAAGGTAtGATTTTATGT

snoRNA + intron

RetroGene derived from H/ACA snoRNA

Evolution's cauldron: duplication, deletion, and rearrangement

Tools -Convert

Tools-Convert

Tools -LiftOver

Tools -liftOver

Paste Data

Tools -liftOver

Tools -liftOver

Track Type Annotation TrackSQL 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

Intersect with snoRNA/microRNA

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 ！