[Ngasp-help] Re: nGASP manuscript

[Tristan Fiedler]

Dear Jonathan,

Thank you very much for commenting on the manuscript.  We are reviewing
your points now.

Sincerely,

Tristan
---
Tristan J. Fiedler, M.Sc., Ph.D.
Assistant Vice President for University Advancement
Research Assistant Professor - Department of Biological Sciences
Florida Institute of Technology
150 W. University Blvd
Melbourne, FL 32901

email : fiedler at fit.edu
office : 321 674 7723
cell : 321 432 0721




>
>> 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
>> <mailto:ngasp-help at wormbase.org>
>>
> A few minor points.
>
> The nGASP analysis team is probably already aware of this, but I just want
> to mention that the Brugia malayi annotation associated with the Science
> publication
> used JIGSAW and included Fgenesh and Augustus as input. I realize that
> the versions
> of Fgenesh and Augustus are likely very different, but some comparison
> of the annotations could be useful in highlighting potential limitations
> in the initial
> publication.
>
> The JIGSAW performance results reported in the text don't use the
> same inputs as are proposed for generating the new annotations, was a
> performance
> comparison done using just the three proposed input programs to confirm
> comparable
> performance?
>
> I would be curious to know if the combiners were more robust for the
> genes with
> less common hexamers or they essentially suffered the same fate.  I
> would guess that
> they would suffer the same problem as the input, but I don't know if it
> was mentioned
> in the text.
>
> I also wish to offer my assistance if needed to address any difficulties
> in using JIGSAW
> to combine output from the other programs.
>
> Typos:
> "Johnathan" should be "Jonathan"
> My address is
> Lawrence Livermore National Laboratory, PO Box 808, L-174, Livermore,
> CA, 94551, USA
>
> Regards,
>
>   Jonathan
>
>
>
>