PeptideSieve

[wooyeah]

Dear all,

I am using PeptideSieve, does anybody know the format of input txt
file that contain peptide sequence rather than protein fasta file?

Thanks
Xuan

[Luis Mendoza]

Hello Xuan,

I am told that the format for the text file should be:

Unique_Peptide_Identifier KTHEPEPTIDERW

one peptide per line.  You must also include both flanking aminoacids in the peptide sequence (in the example line above, the actual peptide is THEPEPTIDER). Also, make sure that each peptide identifier is unique, and that it contains no spaces.

Hope this helps,

--Luis

--

You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To post to this group, send email to spctools...@googlegroups.com.
To unsubscribe from this group, send email to spctools-discu...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.

[Xuan Wang]

Hi Luis,

Thank you so much for that!
What do you mean by Unique_Peptide_Identifier? Any number_letter combination?
Are the flanking aminoacids for all peptides the same as in your example: K___W?

Thanks again,
Xuan

2009/12/17 Luis Mendoza <lmen...@systemsbiology.org>

--
Xuan

[Luis Mendoza]

Hi Xuan,

Yes, I believe any number/letter combination works (e.g. MyPeptide001 etc).  The flanking aminoacids are needed to help determine the enzyme cleavage efficiency; in my example they are K and W, but will be unique/different for each peptide in your list.

Cheers,

--Luis

[Xuan Wang]

Thanks Luis! Is there any way I can find those flanking aminoacids?

2009/12/17 Luis Mendoza <lmen...@systemsbiology.org>

--
Xuan