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 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

Query 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: (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)

Search Result Position zoom in/out Restriction Enzyme mRNA Conservation SNPs

Display option

Gen Browser Query (x)

Gen Browser Results #1 (x)

Gen Browser Results #2 (x)

Gen Browser Details (x)

Gen Browser Syntax (x) Entire chromosome – chr7 (all of chromosome 7) Cytological band – 20p13 (region for band p13 on chr 20) Chromosomal coordinate range – chr3: (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)

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 (…)

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

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

ENCODE Query+Results

ENCODE Details hg16

ENCODE Details hg17

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

Blat Query Query sequence Upload file

Blat Results Browser viewDetail view

Blat Result Browse

Blat Result Details

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

Table Browser Query

Table Browser Results

Table Browser Options Describe Table Schema – schema for SQL table format Filter – regular expression filter – range control Intersection?? Correlation?? Summary Statistics

Table Browser Schema

Table Browser Filter

Table Browser Intersection??

Table Browser Correlation??

Table Browser Summary Statistics

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

Gene Sorter Query

Gene Sorter Results

Gene Sorter Details #1

Gene Sorter Details #2

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

PCR PCR: polymerase chain reaction ，大量複製特定的 DNA 序列

In Silico PCR Query Two primer sequence Max product size Number of match

In Silico PCR Results Melting temperature Match in uppercase Mismatch in lowercase Forward primer Reverse primer

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

Protein Browser Query Swiss-Prot/TrEMBL protein ID

Protein Browser Tracks polarityhydrophobicity cysteinesglycosylation

Protein Browser Histograms

Protein Browser 3D structures

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

IX. Downloads Offers downloads to complete genomes – Human – Chimpanzee – Rhesus – Dog – Cow – Mouse – Rat – Opossum – Chicken