<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Tomas,<div><br></div><div>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.</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Baskerville; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-family: Baskerville; font-size: 14px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Cheers,</div><div><br></div><div>Tristan </div><div><br></div><div><div><font class="Apple-style-span" color="#000066"><b>FL Tech Physics & Space Sciences Ortega Telescope Dedication</b></font></div><div><a href="http://research.fit.edu/pssevent">http://research.fit.edu/pssevent</a></div><div><br></div><div><font class="Apple-style-span" color="#339900"><b>FL Tech Biological Sciences Reunion & Symposium</b></font></div><div><a href="http://research.fit.edu/biologysymposium">http://research.fit.edu/biologysymposium</a></div></div><div>--</div><div>Tristan J. Fiedler, M.Sc., Ph.D.</div><div>Assistant Vice President of Advancement</div><div>Research Assistant Professor</div><div>Department of Biological Sciences</div><div>Florida Institute of Technology</div><div>150 W. University Blvd</div><div>Melbourne, FL 32901</div><div><br></div><div>e<span class="Apple-tab-span" style="white-space: pre; "> </span><a href="mailto:fiedler@fit.edu">fiedler@fit.edu</a></div><div>o<span class="Apple-tab-span" style="white-space: pre; "> </span>321 674 7723</div><div>c<span class="Apple-tab-span" style="white-space: pre; "> </span>321 432 0721</div><div><br></div><br></div></div></span></p></div></span></span></span></span></span></span><span><img height="50" width="348" src="cid:BE6734BC-25A1-4C5E-848F-915AEDF2F797@fit.edu"></span> </div><br><div><div>On Jul 22, 2008, at 5:35 PM, Tomas Vinar wrote:</div><br class="Apple-interchange-newline"><div dir="ltr">Hello,<br><br>The paper is a very nice summary of the experiment. I have very few comments and corrections.<br><br>Corrections in Table 1: <br>- Augustus entry: there is only one author (Stanke), so writing "Stanke et al." is perhaps not the best<br> - 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.<br><br>Other comments:<br><br>- 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.<br> <br>- 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. <br> <br>- 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<br><br>- 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 <br> <br><div class="gmail_quote">On Wed, Jul 16, 2008 at 1:26 PM, Dr. Tristan J. Fiedler <<a href="mailto:fiedler@fit.edu">fiedler@fit.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div style=""><font face="Helvetica" size="5"><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" target="_blank"><font face="Helvetica" size="5"><span style="font-size: 18px;">ngasp-help@wormbase.org</span></font></a><font face="Helvetica" size="5"><span style="font-size: 18px;"><br> <br>Yours sincerely,<br><br>The nGASP analysis team.</span></font><div><font face="Helvetica" size="5"><span style="font-size: 18px;"><br></span></font></div><div><font face="Helvetica" size="5"><span style="font-size: 18px;"></span></font></div> </div><br><div style=""><div><font face="Helvetica" size="5"><span style="font-size: 18px;"></span></font></div></div><br></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------<br> Tomas Vinar, Postdoctoral Researcher<br>Biological Statistics and Computational Biology<br>Cornell University<br>E-mail: <a href="mailto:tv35@cornell.edu">tv35@cornell.edu</a><br>Office: 169 Biotechnology Building<br>Work Phone: +1-607-255-7430 </div></div><br></div></body></html>