Searching with a sequence using BLAT or BLAST

If you have a sequence, but you are not sure what the gene name or ID in Ensembl is, you can align it to the genome with BLAST or BLAT.

Aligning your sequence with BLAST or BLAT


InformationBLAT vs BLAST ... What's the Difference?                

BLAT (The BLAST-Like Alignment Tool) is fast, but it demands more exact matches.  BLAST will allow lower-scoring hits, and allows more gaps in alignments.  You'll get more hits with BLAST (but it may be slower).



Try it!  The beginning of the MTAP4 gene sequence is shown.  Copy it and move on to the steps below.




 BLAT with the MTAP4gene sequence

  1. Click on the BLAST/BLAT link at the top of the page (circled in red in figure).
  2. Paste your sequence into the box [A].  
  3. Check the options are correct. For example, we have selected Homo sapiens as the species to search against and the BLAT search tool because we're looking for an identical match.
  4. Click 'Run' [B]