TBLASTn and Protein Sequence Analysis

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Revision as of 19:03, 22 February 2011 by Dycoughtreydavenport (talk | contribs) (When Nucleotides Don't Work)
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When Nucleotides Don't Work

Occasionally BLASTing genes with just a nucleotide sequence doesn't work. This can be due to a number of reasons:

  • Lack of conservation between species
  • Incomplete genome database
  • Rearrangement of introns/exons


But assuming that you're working with a gene that should be highly conserved and you have allowed for the exon/intron issue, it may be time to go through some extra steps to make sure everything is working as it should:


First - Check to make sure that your database is made correctly.
  • You should have three additional files made from the original fasta file:


Second - Check that your commands are entered correct.
  • Ensure that you are in the correct directory (i.e. Desktop) and BLASTing with the correct file name
  • Sequences being blasted should be in TextEdit and saved without any extension (such as .txt)


'Third - Ensure that the databases/commands are working.
  • Take a known sequence from the database being blasted
  • Typically copy a small portion of the genome into a separate text file
  • Run a BLAST with that sequence against the database you took it from
  • If it doesn't show a hit in the scaffold that you took it from, something is wrong in your programming

Beyond blastn

Why Amino Acids?