<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Tristan,</div><div><br></div><div>the worm genomics meeting in Cambridge kept me busy most of the day. I finally came to read the manuscript. </div><div>I think it is already in pretty good shape. I have a few comments, which you may consider before submitting the manuscript:</div><div><br></div><div>* I missed a more detailed discussion of the annotation dataset that has been used for evaluation. There are a few issues:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>* For unconfirmed genes, how where they predicted? Did any of the compared methods produce these predictions?</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>* Also, for the EST-confirmed genes: these gene models where generated using EST alignments, some manual curation and probably also gene finder predictions. Except the manual curation, the in
put is the same as for cat-3 gene finding. Who knows what the correct gene models are...</div><div> (or something in this direction, you probably have your own thoughts on this).</div><div><br></div><div>* The evaluation for the combiners was done on only the 3' end of the regions. We noticed there is a significant difference for in the performance between the 5' and 3' ends (several percent in transcript level). Hence, the performance on the 3' end and the performance on the whole region are not directly comparable. I don't necessarily want you to redo the evaluation, but at least this should be noted in the main text and also that combiners had about 50% more data for training.</div><div><br></div><div>* Since the result of the paper is that combiners are the method of choice, it would be very interesting to understand how important the accuracy and the choice of the base-gene finders are. It would be really great if you could show some results, indicating whic
h (sub-)set of (the three) gene finders lead to which performance. </div><div><br></div><div>* I really would like the evaluation separately for each category. This would allow us the compare the contributions within the categories more easily. It would be very nice to have, at least in the supplement. </div><div><br></div><div>* One feature that came to our mind that you did not check whether it leads to wrong predictions, is whether there is a gene on the opposite strand. Many gene finders only predict genes on one strand. mGene, for instance, does not.</div><div><br></div><div>* It would be a great service to the gene finding community and also would facilitate reproducibility of this research, if you'd provide the evaluation scripts which lead to exactly the numbers given in the table in the supplement of this paper. (In any case I'd like to get them to evaluate new predictions that we have in the same way.)</div><div><br></div><div>Finally, I'd like to ask you
to reconsider the choice of the Journal. I think it would have a good chance in PLoS Comp Bio or Genome Biology, which I find considerably better suited for this work than BMC Bioinformatics. Why not trying it? </div><div><br></div><div>Thank you and the others for writing the manuscript and organising this competition!</div><div><br></div><div>All the best,</div><div><br></div><div>Gunnar</div><div><br></div><div><br></div><div>On 16.07.2008, at 19:26, Dr. Tristan J. Fiedler wrote:</div><div><br></div><div>Dear nGASP Participants,</div><div><br></div><div>We thank you again for your participation in nGASP.</div><div><br></div><div>The nGASP analysis team has now written up the results of nGASP</div><div>as a paper, which we plan to submit to BMC Bioinformatics.</div><div><br></div><div>As agreed, we are sending you a copy of the draft manuscript </div><div>for your perusal before submission. </div><div><br></div><div>We would be very grateful if you can let
us know if you have any</div><div>major comments on the draft manuscript by Thursday 24th July.</div><div><br></div><div>Comments may be sent to <a href="mailto:ngasp-help@wormbase.org">ngasp-help@wormbase.org</a></div><div><br></div><div>Yours sincerely,</div><div><br></div><div>The nGASP analysis team.</div><div><br></div><div><ngasp_16jul08b_alc.doc></div><div><br></div><div>+-------------------------------------------------------------------+</div><div>Gunnar Rätsch <a href="http://www.fml.mpg.de/raetsch">http://www.fml.mpg.de/raetsch</a></div><div>Friedrich Miescher Laboratory <a href="mailto:Gunnar.Raetsch@tuebingen.mpg.de">Gunnar.Raetsch@tuebingen.mpg.de</a></div><div>Max Planck Society Tel: (+49) 7071 601 820</div><div>Spemannstraße 39, 72076 Tübingen, Germany Fax:
(+49) 7071 601 801</div><div><br></div><div><br></div><div><br></div><div><div>On 16.07.2008, at 19:26, Dr. Tristan J. Fiedler wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;">Dear nGASP Participants,<br><br>We thank you again for your participation in nGASP.<br><br>The nGASP analysis team has now written up the results of nGASP<br>as a paper, which we plan to submit to BMC Bioinformatics.<br><br>As agreed, we are sending you a copy of the draft manuscript <br>for your perusal before submission. <br><br>We would be very grateful if you can let us know if you have any<br>major comments on the draft manuscript by Thursday 24th July.<br><br>Comments may be sent to </span></font><a href="mailto:ngasp-help@wormbase.org"><font cla
ss="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;">ngasp-help@wormbase.org</span></font></a><font class="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;"><br><br>Yours sincerely,<br><br>The nGASP analysis team.</span></font><div><font class="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;"><br></span></font></div><div><font class="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;"></span></font></div><span><ngasp_16jul08b_alc.doc></span></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="Helvetica" size="5"><span class="Apple-style-span" style="font-size: 18px;"></span></font></div></div></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" s
tyle="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><div>+-------------------------------------------------------------------+</div><div>Gunnar Rätsch <a href="http://www.fml.mpg.de/raetsch">http://www.fml.mpg.de/raetsch</a></div><div>Friedrich Miescher Laboratory <a href="mailto:Gunnar.Raetsch@tuebingen.mpg.de">Gunnar.Raetsch@tuebingen.mpg.de</a></div><div>Max Planck Society &nbs
p; Tel: (+49) 7071 601 820</div><div>Spemannstraße 39, 72076 Tübingen, Germany Fax: (+49) 7071 601 801</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div></div><br class="Apple-interchange-newline"></span> </div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><div>+-------------------------------------------------------
------------+</div><div>Gunnar Rätsch <a href="http://www.fml.mpg.de/raetsch">http://www.fml.mpg.de/raetsch</a></div><div>Friedrich Miescher Laboratory <a href="mailto:Gunnar.Raetsch@tuebingen.mpg.de">Gunnar.Raetsch@tuebingen.mpg.de</a></div><div>Max Planck Society Tel: (+49) 7071 601 820</div><div>Spemannstraße 39, 72076 Tübingen, Germany Fax: (+49) 7071 601 801</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div></div><br class="Apple-interchange-newline"></span> </div><br></body></html>