[Ngasp-help] Re: nGASP manuscript

[Tristan Fiedler]

Dear Tomas,

Thank you very much for your comments.  We are currently reviewing  
them.  Through the support and participation of scientists such as  
yourself, the nGASP project has made significant contributions to the  
field of genome annotation.

Cheers,

Tristan

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http://research.fit.edu/pssevent

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http://research.fit.edu/biologysymposium
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Tristan J. Fiedler, M.Sc., Ph.D.
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Research Assistant Professor
Department of Biological Sciences
Florida Institute of Technology
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On Jul 22, 2008, at 5:35 PM, Tomas Vinar wrote:

Hello,

The paper is a very nice summary of the experiment. I have very few  
comments and corrections.

Corrections in Table 1:
- Augustus entry: there is only one author (Stanke), so writing  
"Stanke et al." is perhaps not the best
- ExonHunter entry: there are two authors, so it would be nicer to  
write Brejova and Vinar (instead of Vinar et al.), or at least please  
change this to Brejova et al.

Other comments:

- in abstract: "There was a tie for the third place..." -> this  
sentence implies that cross-species gene finding does not work in C.  
elegans. That may be a very sensitive point with some referees, and I  
don't feel that the corresponding section in the "results" gives good  
enough discussion on this subject. I would remove the sentence from  
the abstract as to not immediately make it a discussion point,  
especially if better analysis cannot be made.

- in results: comparisons between EGASP and nGASP numbers. I am not  
sure that the direct comparison of numbers between EGASP and nGASP is  
a good idea. From various experiments in past, it seems clear that the  
absolute numbers in Sn and Sp can change dramatically depending on  
particular testing set, even within species. Considering that there  
are some substantial differences in methodologies between EGASP and  
nGASP, while comparing the absolute numbers can give some information  
on general trends, I don't think some of the conclusions can be  
supported by the data, especially ones derived from comparison of gene  
level sensitivities and specificities.

- short table giving overview of numbers of genes/exons/bases and  
basic comparison of EGASP and nGASP data sets (e.g., exon lengths,  
intron lengths, exon numbers, etc.) would be useful

- Table 3: Why gene Sn is given only to 1 decimal digit, while all the  
other numbers are given to 2 decimal digits? Also, I am not sure how  
much it is justified to give the data to 2 decimal digit precision,  
since  0.01 is not likely to be anywhere near to statistically  
significant difference in any of the measures

On Wed, Jul 16, 2008 at 1:26 PM, Dr. Tristan J. Fiedler  
<fiedler at fit.edu> wrote:
Dear nGASP Participants,

We thank you again for your participation in nGASP.

The nGASP analysis team has now written up the results of nGASP
as a paper, which we plan to submit to BMC Bioinformatics.

As agreed, we are sending you a copy of the draft manuscript
for your perusal before submission.

We would be very grateful if you can let us know if you have any
major comments on the draft manuscript by Thursday 24th July.

Comments may be sent to ngasp-help at wormbase.org

Yours sincerely,

The nGASP analysis team.






-- 
--------------------------------------------------------------------------
Tomas Vinar, Postdoctoral Researcher
Biological Statistics and Computational Biology
Cornell University
E-mail: tv35 at cornell.edu
Office: 169 Biotechnology Building
Work Phone: +1-607-255-7430

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