peptides prediction for the whole proteome
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zeyu sun
Jul 30, 2012, 10:11:25 AM7/30/12
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Hi,
I'm wondering if any one here know how to predict all tryptic peptides from the whole E.coli proteome. There are tools like PeptideCutter for proteolytic prediction, but it can only cut one protein at each time. Any tools around that can take the whole FASTA database and output a list of tryptic peptides along with their masses?
thank you very much!
sunsun
I'm wondering if any one here know how to predict all tryptic peptides from the whole E.coli proteome. There are tools like PeptideCutter for proteolytic prediction, but it can only cut one protein at each time. Any tools around that can take the whole FASTA database and output a list of tryptic peptides along with their masses?
thank you very much!
sunsun
Amit Yadav
Jul 30, 2012, 10:46:29 AM7/30/12
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Hi
You can try digestdb.exe (comes with TPP)Regards,
Amit Kumar Yadav
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zeyu sun
Jul 30, 2012, 8:59:35 PM7/30/12
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thank you! actually I found another nice program the ProteinDigestionSimulator, http://omics.pnl.gov/software/ProteinDigestionSimulator.php. Both should work!
sunsun
sunsun
A Hill
Jul 31, 2012, 1:35:27 PM7/31/12
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You may also want to check out DBToolkit: http://code.google.com/p/dbtoolkit.
Regards,
Andrew.
On Monday, July 30, 2012 8:59:35 PM UTC-4, sunsun wrote:
Regards,
Andrew.
On Monday, July 30, 2012 8:59:35 PM UTC-4, sunsun wrote:
thank you! actually I found another nice program the ProteinDigestionSimulator, http://omics.pnl.gov/software/ProteinDigestionSimulator.php. Both should work!
sunsun
On Mon, Jul 30, 2012 at 10:46 PM, Amit Yadav
Hi
You can try digestdb.exe (comes with TPP)
Regards,
Amit Kumar Yadav
On Mon, Jul 30, 2012 at 7:41 PM, zeyu sun
Hi,
I'm wondering if any one here know how to predict all tryptic peptides from the whole E.coli proteome. There are tools like PeptideCutter for proteolytic prediction, but it can only cut one protein at each time. Any tools around that can take the whole FASTA database and output a list of tryptic peptides along with their masses?
thank you very much!
sunsun
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