I have a 492kb fasta file and I tried to convert it to faşta.pro with fasta_pro for X!Tandem.
However, I see a line that says 'db type plain' in the command line. Also, faşta_pro.exe stops working when I enter the command for faşta_pro.
What can I do to solve this problem?
PS: I was successful while working with 30kb file.
Hi Cansu,
X!Tandem does work with generic fasta files so maybe it would be worth just using the fasta as it is instead of converting it (which I assume is what fasta_pro.exe does?). From the notes on GPM, the fasta.pro format is more for reading speed which can be an issue if you have a HUGE fasta file e.g. 100's of MBs. With a 492 kb file, it will be fine if you stick with a normal fasta format. However, if you need to convert it, the only issue I would guess is that the fasta you're trying to convert is not in the format that fasta_pro.exe is expecting.
Dave
As Dave mentioned, you do not need to convert fasta file to fasta_Pro.exe . fasta -Pro.exe makes a more compact file that is faster for X!Tandem to search. If you need to convert the file, make sure your file in a proper format: fasta.pro
Simply typing:
fasta_pro.exe /path/to/sequence.fasta
will create an indexed file at the following location:
/path/to/sequence.fasta.pro (or in the current directory ... not sure).
Surely, for such a small file it is not necessary to create an index, but if it is proof of principle and should be used with larger files in the future, it makes sense to establish the complete workflow up front.
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