A Gentle Introduction to UCSC Genome Browser

1. A Gentle Introduction to UCSC Genome Browser 陳任志, 游岳齊

2. 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

3. 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

4. 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

5. Chimp:黑猩猩 Rhesus:恆河猴 Opossum:負鼠 X. tropicalis:蛙 Tetraodon:河豚 Fugu:河豚

6. Display image width Assembly date

7. 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 telomere) • mRNA, EST, or STS marker • Keywords from the GenBank description of an mRNA (huntington)

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

9. Display option

10. 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 (…)

11. 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

12. 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

13. ENCODE Query+Results

14. ENCODE Details hg16

15. ENCODE Details hg17

16. 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

17. Blat Query Query sequence Upload file

18. Blat Results Browser view Detail view

19. 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

20. Table Browser Query

21. Table Browser Results

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

23. Table Browser Schema

24. Table Browser Filter

25. Table Browser Summary Statistics

26. 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

27. Gene Sorter Query

28. Gene Sorter Results

29. Gene Sorter Details #1

30. Gene Sorter Details #2

31. 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

32. PCR PCR: polymerase chain reaction，大量複製特定的DNA序列 http://members.aol.com/BearFlag45/Biology1A/LectureNotes/lec24.html

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

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

35. 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

36. Protein Browser Query Swiss-Prot/TrEMBL protein ID

37. Protein Browser Tracks polarity hydrophobicity cysteines glycosylation

38. Protein Browser Histograms

39. Protein Browser 3D structures

40. 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

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