Professional Documents
Culture Documents
http://genome.ucsc.edu/
Louis Tang
Bioinformatics R&D
National Genotyping Center
Academia Sinica.
louis@ibms.sinica.edu.tw
Quick Overview of features on
genomic regions
End of The Human Genome War
W. James Kent
Coordinate Genome Assembly
Annotation Tracks Gene
Regulation
Variation
Expression
More…
Annotation Tracks
Coordinate
Everlasting Assembly
Ever-Changing Tracks
http://genome.ucsc.edu/
Coordinate
chr3:1,000,000-2,000,000
chr3:1,000,000+2000
chr3:1,000,000-1,001,999
Landmark
chromosome
Gene
SNP
STS EST
Cytogenetic band
chr7
chr7:1-158,821,424
20q12
chr20:37,100,001-41,100,000
apoe
chr19:50,100,879-50,104,490
rs328
chr8:19864004
±250
chr8:19,863,754-19,864,254
D16S2837
±100,000
chr16:81,020,163-81,220,399
Landmark1;Landmark2
Landmark1 Landmark2
rs328;rs316
chr8:19,864,004 chr8:19,862,716
Sort
chr8:19,862,716-19,864,004
Author
McAndrew,P.E.
Browser Graphic
Track Control
Mark
Gene
>>>>>> >>>>
PDB
>>>>>> >>>>
Reviewed
>>>>>> >>>>
RefSeq Provisional
>>>>>> >>>>
Non-RefSeq
>>>>>> >>>>
Alignment
TAACCAGCTGCCCAA--------TAGAAACTACGAGAGACAACAGGGAGT
||||| ||||||||| ||||||| | ||||||||||
TAACCAGCTGCCCAACTGTAGAAACTACCAACTCATTTCGAACAGGGAGT
Wiggle
Mapping and Sequencing
Phenotype and Disease Association (OMIN)
Expression
Comparative Genomics
ENCODE Pilot
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Practice
http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
Where is the Sequence?
RefSeq Gene
SNP
Browser Graphic Download
chr8:19,863,754-19,864,254
rs328
McAndrew,P.E.
?
AACTAGAAATCAGTCAACAAATTGGATGCTTAGGATAAATTCAAGAACTG
AGTAGAGAAATAAAGCTTAATGAATGACCTTTTGGGCTCCTTCCAGTTCC
AAGGTTTTAGTATTCTAAAATTTTCGGCACAGAACAACTCCAAATGCTCA
GGAAATAAGAATGAGGTCTGTTTTTAAAAGGTGCAGTTTGGAGCATGTTG
GGTGGATGAGGCTATAAAAAGTGAAGTACGATTTTCAAGGAAAGGAAGCT
GACCAATCAAAGTCTTTTGGGCAGCCCCTCCAGAAATCCAGGTGAAGCCC
GGCTCCAGGCTGAGTTGCTGTTACTCTACACGAAAGCCAGGCCGCTACTT
BLAT
500x
Protein
50x
DNA & RNA
95%
25 bases
Protein
80%
20 amino acids
DNA
mRNA
BLAT’s Guess
DNA (RNA)
Query Genome
DNA DNA
Protein
Query Genome
Protein DNA
6 frames
Protein
Translated RNA
Query Genome
RNA DNA
3 frames 6 frames
Protein Protein
Translated DNA
Query Genome
DNA DNA
6 frames 6 frames
Protein Protein
Query
Genome
Query
Genome
Query
Genome
Query
Genome
Practice
http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
Pretty graphic is good,
but…
I want raw data
Table Browser
Text-based access to features
on genomic regions
Mission
(Hg18, SNP130)
Find all single SNPs on tp53
(uc002gij.2)
Genome Browser Table Browser
Database
Database
Table
Table
Table
Table Table
Genome Browser
Annotation Track
Table Table
Table
Table Browser
Table
Table
Table
Apoe
Start Stop
Genome Browser 50100879 50104490
Table Browser 50100878 50104490
C A C C T C A G A
Biology 1 2 3 4 5 6 7 8 9
Computer 0 1 2 3 4 5 6 7 8
C A C C T C A G A
Biology 1 2 3 4 5 6 7 8 9
Computer 0 1 2 3 4 5 6 7 8
C A C C T C A G A
Biology 1 2 3 4 5 6 7 8 9
Computer 0 1 2 3 4 5 6 7 8
C A C C T C A G A
Biology 1 2 3 4 5 6 7 8 9
Computer 0 1 2 3 4 5 6 7 8
C A C C T C A G A
Biology 1 2 3 4 5 6 7 8 9
Computer 0 1 2 3 4 5 6 7 8
3 Questions
Table?
Output Format?
Filter Criteria?
Table
Output
Practice
hg18
snp130
chr6:1,000,000-1,001,000
Sequence Output
100 extra bases on either stream
Filter Criteria
Positional
Non-Positional
Positional
One-Based
chrX 151073054 151173000
chrX 151183000 151190000
chrX 151283000 151290000
Zero-Based
chrX:151,073,055-151,173,000
chrX:151,183,001-151,190,000
chrX:151,283,001-151,290,000
One-Based
Practice Time
hg18
snp130
chr6:1,000,000-1,500,000
chr6:2,000,000-2,500,000
TP53 = TP53
Item Count: 47
SNP
Gene
SNP
Intersect
Gene
Practice Time
hg18
chr1:1,000,000-2,000,000
Find SNPs(v.130) on sno/miRNA
Zero-Based
chr4 1000000 1005000 myData 200 + 1000100 1004900 100,150,200
name
chr4 1000000 1005000 myData 200 + 1000100 1004900 100,150,200
score (0 ~ 1000)
chr4 1000000 1005000 myData 200 + 1000100 1004900 100,150,200
strand
chr4 1000000 1005000 myData 200 + 1000100 1004900 100,150,200
thickStart thickEnd
chr4 1000000 1005000 myData 200 + 1000100 1004900 100,150,200
color
Red,Green,Blue
0~255
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Mailing List
Subject: in-Silico PCR Min Perfect/Good Match confuses me
From: louis@ibms.sinica.edu.tw
To: genome@soe.ucsc.edu
Date: 04/22/2010 03:24:06 PM
Hi,
On the in-silico PCR input page there are two options: min perfect match
& min good match. There are some explanations on the same page:
…
But how can these two options be specified simultaneously? will one
option be overridden by another?
Louis
Subject: Re: [Genome] in-Silico PCR Min Perfect/Good Match confuses me
From: Galt Barber galt@soe.ucsc.edu
To: genome@lists.soe.ucsc.edu
Date: 04/23/2010 02:50:01 AM
Hi, Louis!
-Galt
"It's been a wonderful stone soup, where
other people have contributed bits,"
- James Kent
http://tiny.cc/d56k6