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A Gentle Introduction to UCSC Genome Browser. 陳任志 , 游岳齊. Options. I. Genome Browser II. ENCODE III. Blat IV. Table Browser V. Gene Sorter VI. In Silico PCR VII. Proteome Browser VIII. Utilities IX. Downloads. I. Genome Browser. Human (Homo sapiens) Genome Browser Gateway - PowerPoint PPT Presentation
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A Gentle Introduction to UCSC A Gentle Introduction to UCSC Genome BrowserGenome Browser
陳任志 , 游岳齊
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
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
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
Chimp:黑猩猩
Rhesus:恆河猴
Opossum:負鼠
X. tropicalis:蛙
Tetraodon:河豚
Fugu:河豚
Assembly date Display image width
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)
Search ResultSearch ResultPosition
zoom in/out
Restriction EnzymemRNA
ConservationSNPs
Display option Display option
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 (…)
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
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
ENCODE Query+ResultsENCODE Query+Results
ENCODE Details hg16ENCODE Details hg16
ENCODE Details hg17ENCODE Details hg17
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
Blat QueryBlat Query
Query sequence
Upload file
Blat ResultsBlat Results
Browser viewDetail view
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
Table Browser QueryTable Browser Query
Table Browser ResultsTable Browser Results
Table Browser OptionsTable Browser Options
Describe Table Schema– schema for SQL table format
Filter– regular expression filter– range control
Intersection??Correlation??Summary Statistics
Table Browser SchemaTable Browser Schema
Table Browser FilterTable Browser Filter
Table Browser Summary Table Browser Summary StatisticsStatistics
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
Gene Sorter QueryGene Sorter Query
Gene Sorter ResultsGene Sorter Results
Gene Sorter Details #1Gene Sorter Details #1
Gene Sorter Details #2Gene Sorter Details #2
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
PCRPCRPCR: polymerase chain reaction,大量複製特定的 DNA序列
http://members.aol.com/BearFlag45/Biology1A/LectureNotes/lec24.html
In Silico PCR QueryIn Silico PCR Query
Two primer sequence
Max product size Number of match
In Silico PCR ResultsIn Silico PCR Results
Melting temperature
Match in uppercase
Mismatch in lowercase
Forward primer Reverse primer
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
Protein Browser QueryProtein Browser Query
Swiss-Prot/TrEMBL protein ID
Protein Browser TracksProtein Browser Tracks
polarity hydrophobicity
cysteines glycosylation
Protein Browser HistogramsProtein Browser Histograms
Protein Browser 3D structuresProtein Browser 3D structures
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
IX. DownloadsIX. Downloads
Offers downloads to complete genomes– Human– Chimpanzee– Rhesus– Dog– Cow– Mouse– Rat– Opossum– Chicken