[Ngasp-help] Re: nGASP manuscript

[Jonathan E. Allen]

> 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