Customized databases

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Carbon Member
Carbon Member
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Joined: Thu Oct 20, 2011 3:50 am

Customized databases

Postby ganjirakesh » Mon Oct 24, 2011 4:03 am

Hi all,
IN the link I have given below,
I happened to read certains facts like customized database, concatenated database.
In this paper, they have analysed their MS/MS data with a customized database to identify the proteins.
Can anyone please tell me as how these custmized databases are created? How can one search their MS data with these customized databases.

Thanks in advance.

Angiotensin Member
Angiotensin Member
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Joined: Tue Sep 20, 2011 2:50 am

Postby Artur » Mon Oct 24, 2011 4:46 am

databases are generally stored as a *.fasta file containing protein or nucleic acid sequeces.
As a example of making concatenated database, you can retrieve some protein entries (for example for one organism) as a fasta file from Swissprot, and open it i a good text editor (e.g notepad++). Then you can add your own sequences, keeping in mind data structure(the header before sequence, no whitespaces at end of the lines).
Then you have to add these file to your search engine, the exact way depends of which engine you use.

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