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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If, for any of these reasons, you aren't getting any hits, it might be time to make sure you're doing it right: | 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. | + | ::='''''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''''' - Check that your commands are correct | + | ::'''''Second''''' - Check that your commands are correct. |
| − | :::** | + | :::*Ensure that you are in the correct database and BLASTing with the correct file name |
| + | :::*Sequences being blasted should be in TextEdit and saved without any extension (such as .txt) | ||
| + | |||
| + | ::''''Third''''' - | ||
== Beyond blastn == | == Beyond blastn == | ||
== Why Amino Acids? == | == Why Amino Acids? == | ||
Revision as of 18:54, 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:
- =First - Check to make sure that your database is made correctly.=
- Second - Check that your commands are correct.
- Ensure that you are in the correct database and BLASTing with the correct file name
- Sequences being blasted should be in TextEdit and saved without any extension (such as .txt)
- Second - Check that your commands are correct.
- 'Third -
