The UCSC Genome Browser

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The UCSC Genome Browser

• From Men to Mice

WJ Kent, C Sugnet, T Furey, T Pringle, M
Schwartz, R Baertsch, R Weber, K Roskin, D
Thomas, S Rogic, M Diekhans, F Hsu, D Karolchik,
D Haussler
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(No Transcript)
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Cardiac Troponin T2
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Comparative Genomics at BMP10
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Normalized eScores
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Mouse/Human Synteny
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Track Options Filters
Mini-buttons bring up track options such as
those for spliced EST track below.
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Which EST to Sequence?
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MGC ESTS Drawn in Red
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DNA Coloring
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Coloring CRYGD Start
gctcgttcaggggtaaaggtgtattctagatCCACAACAAGCCCCGTGGT
CTAGCACAGC AAAGAGAAAAAAAGAGAACACGAAAATGCCCTTGCTCCC
CTCCGGGGGCCCCTTTTGTGC GGTTCTTGCCAACGCAGCAGCCCTCCTG
CTATATAGCCCGCCGCGCCgCAGCCCCACCCG
CTCAGCGCCGCCGCCCCACCAGCTCAGCACCGCCGTGCGCCCAGCCAGCC
ATGGGGAAGG TGAGCCCAGCCTGCGCCCCGGGACCCCGGAGCTTCCTCC
ATCGCGGGGGCCAGAGACTGG GGCAGGAGCAGGCCTGTGAGACCTCGCC
TTGTCCCGCCTTGCCTTGCAGATCACCCTCTA
CGAGGACCGGGGCTTCCAGGGCCGCCACTATGAATGCAGCAGCGACCACC
CCAACCTGCA GCCCTACTTGAGCCGCTGCAACTCGGCGCGCGTGGACAG
CGGCTGCTGGATGCTCTATGA GCAGCCCAACTACTCGGGCCTCCAGTAC
TTCCTGCGCCGCGGCGACTATGCCGACCACCA
GCAGTGGATGGGCCTCAGCGACTCGGTCCGCTCCTGCCGCCTCATCCCCC
ACGTGAGTAC ATCCTCAAGTCAGGACCCAGGCCCTCAGGACACTCACTG
GAtgGTTTCAAGCAAAAGTTA AACATTAGAAGTAGTGATCAGTcacaat
aaCTGAGAGTGGACAAAAGATGAACTATAGTG
GATTAAGTCAATAGagttTGCTCCCCACATAAGCAAAGTATTACCCAGAC
AcCAGTTAAT caCAATTAATCCACAAATATGTATTGAGTAGGAATGTGT
CTCCTGCCctAGGGGTTGTAT
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Gene Expression Tracks
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Alt Splicing Tracks
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Complex Transcription
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Add Your Own Tracks

• Users can extend the browser with their own
  tracks.
• User tracks can be private or public.
• No programming required.
• GFF, GTF, PSL or BED formats supported
• chrom start end name strand score
• chr1 1302347 1302357 SP1 800
• chr1 1504778 1504787 SP2 980

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The Underlying Database

• Power users and bioinformaticians sometimes want
  underlying database.
• There is a table for each track.
• Larger tracks have a table for each chromosome.
• Format of a track table generally similar to
  add-your-own track formats.
• Pieces of database available from tables
  browser.
• Whole database available as tab-separated files.

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Parasol and Kilo Cluster

• UCSC cluster has 1000 CPUs running Linux
• 1,000,000 BLASTZ jobs in 25 hours for mouse/human
  alignment
• We wrote Parasol job scheduler to keep up.
• Very fast and free.
• Jobs are organized into batches.
• Error checking at job and at batch level.

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Acknowledgements
NHGRI, The Wellcome Trust, HHMI, NCI, and
Taxpayers in the US and worldwide. Whitehead,
Sanger, Wash U, Baylor, Stanford, DOE, and the
international sequencing centers. NCBI, Penn
State, Ensembl, Genoscope, The SNP Consortium, UC
Berkeley, LBL, LLL, Riken, The Mammalian Gene
Collection, Softberry, IMIM, Affymetrix,
Perlagen, Rosetta, the Mouse Homology Group The
thousands of people who worked on the sequence
and annotations