A Gentle Introduction to UCSC Genome Browser

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A Gentle Introduction to UCSC Genome Browser

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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

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I. 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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Query
Clade ??????????? vertebrate???? deuterostome
??? insect?? nematode??
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Chimp??? Rhesus??? Opossum?? X.
tropicalis? Tetraodon?? Fugu??
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Display image width
Assembly date
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• Entire chromosome
• chr7 (all of chromosome 7)
• Cytological band
• 20p13 (region for band p13 on chr 20)
• Chromosomal coordinate range
• chr31-1000000 (first million bases of chr 3,
  counting from p arm telomere)
• mRNA, EST, or STS marker
• Keywords from the GenBank description of an mRNA
  (huntington)

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Search Result
Position zoom in/out
Restriction Enzyme
mRNA
Conservation
SNPs
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Display option
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Gen Browser Query (x)
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Gen Browser Results 1 (x)
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Gen Browser Results 2 (x)
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Gen Browser Details (x)
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Gen Browser Syntax (x)

• Entire chromosome
• chr7 (all of chromosome 7)
• Cytological band
• 20p13 (region for band p13 on chr 20)
• Chromosomal coordinate range
• chr31-1000000 (first million bases of chr 3,
  counting from p arm telomere)
• mRNA, EST, or STS marker
• Keywords from the GenBank description of an mRNA
  (huntington)

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II. 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 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 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 QueryResults
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ENCODE Details hg16
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ENCODE Details hg17
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III. Blat

• To quickly find sequences of 95 and greater
  similarity of length 40 bases or more
• BLAST-Like Alignment Tool, not BLAST
• Use Paste in a query sequence to find its
  location in the the genome
• takes up just under 1 GB of RAM

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Blat Query
Query sequence
Upload file
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Blat Results
Browser view
Detail view
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Blat Result Browse
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Blat Result Details
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IV. 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 Query
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Table Browser Results
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Table 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 Schema
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Table Browser Filter
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Table Browser Intersection??
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Table Browser Correlation??
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Table Browser Summary Statistics
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V. 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 Query
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Gene Sorter Results
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Gene Sorter Details 1
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Gene Sorter Details 2
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VI. 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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PCR
PCR polymerase chain reaction,???????DNA??
http//members.aol.com/BearFlag45/Biology1A/Lectur
eNotes/lec24.html
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In Silico PCR Query
Two primer sequence
Max product size
Number of match
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In Silico PCR Results
Reverse primer
Forward primer
Match in uppercase Mismatch in lowercase
Melting temperature
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VII. 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 Query
Swiss-Prot/TrEMBL protein ID
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Protein Browser Tracks
polarity
hydrophobicity
cysteines
glycosylation
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Protein Browser Histograms
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Protein Browser 3D structures
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VIII. 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 different chromosome as the map is
  refined
• DNA Duster
• formatting tool
• Protein Duster
• formatting tool

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IX. Downloads

• Offers downloads to complete genomes
• Human
• Chimpanzee
• Rhesus
• Dog
• Cow
• Mouse
• Rat
• Opossum
• Chicken