<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-size: medium; font-family: 'Times New Roman', serif; "><span style="mso-spacerun: yes"> </span>1. by view the gff file produced by maker2, I have found most of the predicted gene loci have est matches. but why only 254 gene annotations got by maker2 ?</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div style="font-family: Calibri, sans-serif; font-size: 14px; ">I'd really have to see the results to tell you why.</div></blockquote></blockquote><span id="OLK_SRC_BODY_SECTION"><div><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3"><!-- --><o:p><br><!-- --></o:p></font></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; text-indent: 5.25pt; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">2. in the “non-overlapping ab initio”file, I found sequences are all from augustus_masked prediction. Does the non-overlapping file only include the best gene modes from predicted by both augustus and genemark? <span style="mso-spacerun: yes"> </span>Does it include genemark- or augustus-specific genes ?<o:p></o:p></font></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 14px; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><font class="Apple-style-span" face="Times New Roman,serif">The "non-overlapping" file should have the one with best consensus if there are 3 or more predictors, and the longest one otherwise. It should be able to have augustus and genemark genes. Try it with only genemark and let me know if the file is empty.</font></p></blockquote></blockquote></div></span><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div></body></html>