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A Gentle Introduction to UCSC A Gentle Introduction to UCSC Genome BrowserGenome Browser
陳任志 , 游岳齊
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OptionsOptions
I. Genome Browser II. ENCODE III. Blat IV. Table Browser V. Gene Sorter VI. In Silico PCR VII. Proteome Browser VIII. Utilities IX. Downloads
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I. Genome BrowserI. Genome Browser
Human (Homo sapiens) Genome Browser Gateway
Provides any section of entire human genome Non-Standard Join Certificates
– some sequence joins between adjacent clones in this assembly could not be computationally validated
the sequencing center responsible for the particular chromosome provides an electronic certificate
– should state why the submitter thinks the join is valid
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QueryQuery
Clade: 具有相同祖先的一群生物
vertebrate:脊椎動物
deuterostome:後口類
insect:昆蟲
nematode:線蟲
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Chimp:黑猩猩
Rhesus:恆河猴
Opossum:負鼠
X. tropicalis:蛙
Tetraodon:河豚
Fugu:河豚
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Assembly date Display image width
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Entire chromosome– chr7 (all of chromosome 7)
Cytological band– 20p13 (region for band p13 on chr 20)
Chromosomal coordinate range– chr3:1-1000000 (first million bases of chr 3, counting from p arm t
elomere) mRNA, EST, or STS marker Keywords from the GenBank description of an mRNA (huntington)
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Search ResultSearch ResultPosition
zoom in/out
Restriction EnzymemRNA
ConservationSNPs
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Display option Display option
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II. ENCODEII. ENCODE
Stands for “Encyclopedia Of DNA Elements” Public research consortium to carry out a project
to identify all functional elements in the human genome sequence
Launched by The National Human Genome Research Institute (NHGRI)
Conducted in three phases:– pilot project phase (survey existing methods)– technology development phase (develop new methods)– planned production phase (…)
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ENCODE FormatsENCODE Formats
Browser Extensible Data Format (BED)– for efficient access to genomic annotations
General Feature Format (GFF)– for data where there are a set of linked features
Gene Transfer Format (GTF)– a refinement of GFF that tightens the specification
Multiple Alignment Format (MAF)– a series of multiple alignments in one format
Wiggle Format (WIG)– for continuous-valued data in track format
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ENCODE OptionsENCODE Options
Regions (hg16)– old database (+mRNA, EST, & STS markers)
Regions (hg17)– new database (+mRNA, EST, & STS markers)
Data Status– the current status of ENCODE datasets
Downloads– sequence and annotation data downloads
Submission– for the submission of ENCODE-related data
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ENCODE Query+ResultsENCODE Query+Results
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ENCODE Details hg16ENCODE Details hg16
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ENCODE Details hg17ENCODE Details hg17
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III. BlatIII. Blat
To quickly find sequences of 95% and greater similarity of length 40 bases or more
BLAST-Like Alignment Tool, not BLASTUse: Paste in a query sequence to find its
location in the the genometakes up just under 1 GB of RAM
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Blat QueryBlat Query
Query sequence
Upload file
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Blat ResultsBlat Results
Browser viewDetail view
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IV. Table BrowserIV. Table Browser
To get the data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track
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Table Browser QueryTable Browser Query
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Table Browser ResultsTable Browser Results
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Table Browser OptionsTable Browser Options
Describe Table Schema– schema for SQL table format
Filter– regular expression filter– range control
Intersection??Correlation??Summary Statistics
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Table Browser SchemaTable Browser Schema
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Table Browser FilterTable Browser Filter
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Table Browser Summary Table Browser Summary StatisticsStatistics
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V. Gene SorterV. Gene Sorter
Displays a sorted table of genes that are related to one another
Correlation is color-coded– a highly expressed gene is colored red– a less expressed gene is shown in green
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Gene Sorter QueryGene Sorter Query
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Gene Sorter ResultsGene Sorter Results
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Gene Sorter Details #1Gene Sorter Details #1
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Gene Sorter Details #2Gene Sorter Details #2
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VI. In Silico PCRVI. In Silico PCR
In-Silico PCR searches a sequence database with a pair of PCR primers
Returns: a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair
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PCRPCRPCR: polymerase chain reaction,大量複製特定的 DNA序列
http://members.aol.com/BearFlag45/Biology1A/LectureNotes/lec24.html
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In Silico PCR QueryIn Silico PCR Query
Two primer sequence
Max product size Number of match
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In Silico PCR ResultsIn Silico PCR Results
Melting temperature
Match in uppercase
Mismatch in lowercase
Forward primer Reverse primer
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VII. Protein BrowserVII. Protein Browser
UCSC Proteome Browser Gateway provides a wealth of protein information presented
in the form of graphical images and links to external internet sites– SwissProt information– Proteome browser tracks– Protein property histograms– UCSC links / Domain information– Comparative 3D structures– Pathways / Fasta format
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Protein Browser QueryProtein Browser Query
Swiss-Prot/TrEMBL protein ID
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Protein Browser TracksProtein Browser Tracks
polarity hydrophobicity
cysteines glycosylation
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Protein Browser HistogramsProtein Browser Histograms
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Protein Browser 3D structuresProtein Browser 3D structures
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VIII. UtilitiesVIII. Utilities
Some tools (for preparing input)– Batch Coordinate Conversion (liftOver)
converts genome coordinates and genome annotation files between assemblies
WHY?– occasionally, a chunk of sequence may be moved to an entirely d
ifferent chromosome as the map is refined
– DNA Duster formatting tool
– Protein Duster formatting tool
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IX. DownloadsIX. Downloads
Offers downloads to complete genomes– Human– Chimpanzee– Rhesus– Dog– Cow– Mouse– Rat– Opossum– Chicken