Difference between revisions of "TBLASTn and Protein Sequence Analysis"

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(When Nucleotides Don't Work)
(When Nucleotides Don't Work)
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::'''''First''''' - Check to make sure that your database is made correctly.
 
::'''''First''''' - Check to make sure that your database is made correctly.
 
:::*You should have three additional files made from the original fasta file:
 
:::*You should have three additional files made from the original fasta file:
 +
::'''''Second''''
  
 
== Beyond blastn ==
 
== Beyond blastn ==
  
 
== Why Amino Acids? ==
 
== Why Amino Acids? ==

Revision as of 18:38, 22 February 2011

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


If, for any of these reasons, you aren't getting any hits, it might be time to make sure you're doing it right:

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

Beyond blastn

Why Amino Acids?