How To Make A Random Database Of Peptides Eg In Fasta Format

Question

[kunsz86]

Hi,

I am trying to create a random database of peptides (using only, for example, all combinatorial possibilities of 10 specific amino acids ), and using this as the reference database for Mass spectrometry (MS/MS) identification.

Someone recommended that I create a random library of FASTA files, with an identifier for the peptide sequence, and possibly with mass included somewhere. Does anyone know if there is any software for doing this, or how this can be programmed?

Any other suggestions would be greatly appreciated.

Thanks,

Kun

[Neilfws]

I think what you want is a database of "random" sequences, as opposed to a random database :)

[Ben]

Do you want random sequences or all possible combinations of given amino acids?

[Neilfws]

That was my second thought; not clear from the question what "random" means.

Answer 1

[Josh Herr]

There are three options in Generate Random Dna Sequence Data With Equal Base Frequencies. You can modify these examples to generate random peptides and set the length of the random sequences you need. The PhyloSim package and the first scripting example use R. The other example is in Python.

Answer 2

[Niallhaslam]

There is a pretty comprehensive answer here: http://nsaunders.wordpress.com/2007/07/25/howto-generate-random-sequences-using-emboss-and-perl/

[Neilfws]

Should have remembered that, as I'm the author :)