UCSC$Genome$Browser$and$ ENCODE$tutorialpromoter.bx.psu.edu/Yue_slides.pdf · The Genome Browser...
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UCSC Genome Browser and ENCODE tutorial Feng Yue Assistant Professor Dept. of Biochem & Molecular Biology Penn State School of Medicine,
Transcript of UCSC$Genome$Browser$and$ ENCODE$tutorialpromoter.bx.psu.edu/Yue_slides.pdf · The Genome Browser...
UCSC Genome Browser and ENCODE tutorial
Feng Yue Assistant Professor
Dept. of Biochem & Molecular Biology Penn State School of Medicine,
Outline
• Overview of UCSC genome browser; • Search for a gene/genomic region; • Display a track (gene expression, TF binding sites, histone modificaOon, et al);
• Blat a sequence; • Search for orthologou sequences; • Search for datasets on ENCODE website; • Slides and links available: hSp://www.yuelab.org
UCSC genome browser hSps://genome.ucsc.edu
Display TranscripOon Factor Binding Signals
BLAT: Search a genome
CTCCTAGTCCAGTGGAGGGAGACAAACACCAATCA
Search orthoglous sequence genome.ucsc.edu/cgi-‐bin/hgLiVOver
chr21 32871466 32871500
• QuesOon: Can you find the orthologous regions using a method/too I just showed you? – Hint: you know the genomic sequence…
ENCODE: encyclopedia of dna elements hSps://www.encodeproject.org
