Difference between revisions of "TBLASTn and Protein Sequence Analysis"
From GcatWiki
(→When Nucleotides Don't Work) |
(→When Nucleotides Don't Work) |
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| + | 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: | :::*You should have three additional files made from the original fasta file: | ||
| − | ::'''''Second''''' - Check that your commands are correct. | + | |
| − | :::*Ensure that you are in the correct | + | ::'''''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) | :::*Sequences being blasted should be in TextEdit and saved without any extension (such as .txt) | ||
| − | ::''''Third''''' - | + | |
| + | ::''''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 == | == Beyond blastn == | ||
== Why Amino Acids? == | == Why Amino Acids? == | ||
Revision as of 19:03, 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
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:
- First - Check to make sure that your database is made correctly.
- 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)
- Second - Check that your commands are entered correct.
- '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
- 'Third - Ensure that the databases/commands are working.
