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The UCSC Genome Browser

Search with BLAT

You can use sequences that you retrieve from the browser or nucleotide sequences that you have obtained from other sources to run a BLAT on the UCSC Genome Browser site.  BLAT is not quite the same as a genomic BLAST.  It works by keeping an index of the target genome in memory, rather than the entire genome sequence itself.

To try a BLAT from the ACE gene view we've been working with:

  • Click on the transcript graphic in the GENCODE Comprehensive Transcript Set part of the browser view to open the Description and Page Index page.

 

  • Now click on either the Genomic Sequence or the mRNA sequence links in the Sequence menu

 

Note: If you click on Genomic Sequence, you can add bases up- or downstream, but be sure to keep your sequence total length under 25,000 bases.  BLAT cannot align anything larger than that.  This is why it is sometimes easier to align the mRNA sequence instead of the genomic sequence.

  • Once you have a view of the FASTA formatted sequence(s) in your web browser window, use a "select all" command to highlight the FASTA sequece, then copy it.
  • Now click on the Tools menu in the UCSC Genome Browser menu bar and choose Blat (first option in the Tools menu)
  • Paste your sequence in the text box, and select the species genome, assembly, query type (DNA, RNA, protein, or let BLAT guess it for you); select your sort output and output type.  The hyperlink output type is most useful for viewing results.
  • Click submit 
    • Note: if you click "I'm feeling lucky", like Google, you will only get the best result, viewed in the Genome Browser graphic view.  Though cute, this is not always very helpful.
  • You can also use the File Upload field to upload your own sequence file, in plain text format.

Screen shot of BLAT Search Results

 

  • If you have used sequence from a known gene or known genomic region, you will likely have one very high-scoring match, followed by others of lesser scores.
  • Note that you have matches on both forward and reverse strands of the genome in the region defined
  • Click on the browser link for any match to see a graphic view of the BLAT alignment in the Genome Browser
  • Click on the details link to see a series of "blocks" of matching sequence, followed by side-by-side alignments of the query sequence (your input) and the target hit from the genome.