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UCSC Archaeal genome browser

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UCSC Archaeal genome browser Powered By Docstoc
					UCSC Archaeal genome
      browser




        September 19, 2006
   David Bernick, Aaron Cozen and
             Todd Lowe
                       Agenda
 Basic searches with the Archaea Genome browser
     Text searches
     Sequence searching - BLAT, short sequences
     In-silico PCR
     Hands-on session - Navigation and searching
 Advanced features
     Table Browser
     Custom tracks
     Conservation tracks and inter-species navigation
     Hands-on session - Table Browser and Custom tracks
UCSC Archaeal Genome Browser
        http://archaea.ucsc.edu
UCSC Archaeal Genome Browser
 sample search for “regulatory proteins”
 coordinates and
annotated direction,
 using Genbank,
  Tigr and Rfam

     predicted
   promoters and
    terminators




       conservation
Short sequence searching
Short sequence input
Sequence searching - BLAT




   search with either nucleotide or protein sequence
BLAT results
BLAT result - detail
BLAT result - browser
BLAT search - multiple hits
BLAT- multiple hit response
BLAT - tRNA D arm
in-silico PCR primer search
in-silico search results
UCSC Genome Browser
    PCR Results -
    UCSC Genome Browser
           review
 Searching
   Text annotation- name and description
   Short sequence
   Blat - protein or nucleotide sequence
   in-silico PCR

				
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