thanks Brian,
I saw the pdf but i am still unable to calculate evalue for some
cases. Problem lies with small fasta database(100 sequences) where i dont
get enough candidate peptides, in cases two or three. i am unable to draw a
straight line of log(#results). I m surprised that x!tandem still provides
evalues for such cases as i tested with the same small database. How does
X!tandem tackle this problem?
2009/10/21 Brian Searle <[email protected]>
>
> Hi,
>
> Here's a short talk I gave years ago for a user meeting on X!Tandem:
> www.proteomesoftware.com/XTandem_edited.pdf
>
> Pages 11-14 discuss how the e-value is calculated. What do you mean
> exactly by data set/sequences? The e-value is not dependent on the
> number of spectra in a data set as individual spectra are not scored
> together (although PeptideProphet will have a harder time trying to
> make sense of small data sets). The e-value can be database dependent
> and it may not work well for a 100 sequence FASTA database if you're
> employing high-mass accuracy peptide selection criteria.
>
> Best, Brian
>
>
> On Oct 20, 3:24 am, dhirendra <[email protected]> wrote:
> > hi,
> > can anyone provide me detailed explanation about how the X!tandem e-
> > value is calculated and how good is it for small dataset of say 100
> > sequences?
>
> >
>
--
Regards:
Dhirendra Kumar
Project assistant
IGIB
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