This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Make A Random Database Of Peptides Eg In Fasta Format

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

random fasta mass-spec
• 5,627 views • link
updated by Niallhaslam Niallhaslam • written by kunsz86 • kunsz86

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

• 0 views • link
written by Neilfws Neilfws

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

• 0 views • link
written by Ben Ben

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

• 0 views • link
written by Neilfws Neilfws

2 answers

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.

• 1 views • link
written by Josh Herr Josh Herr

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

• 0 views • link
written by Niallhaslam Niallhaslam

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

• 0 views • link
written by Neilfws Neilfws

Log in to answer this question.

More posts like this