<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">It is not the first time I see that, but I have an annotation launched with the option keeps_pred=0 that contains gene models with AED score equal to 1. As far as I understand, AED score to 1 means there is no evidence support. So it should be purely abinitio without any line of evidence in front of this prediction.</div><div class="">But as it is written in “Michael S-Cambell et <i class="">al.</i>, Genome Annotation and Curation Using MAKER and MAKER-P, Current Protocols in Bioinformatics, 2014” page 4.11.36 about the the keep_preds option:</div><div class=""><b class="">"MAKER rejects models that do not have at least some form of evidence support.” </b>Setting<b class=""> </b>keep_preds to 1 “remove the evidence support requirement”.</div><div class=""><br class=""></div><div class="">So, how should I understand my results? Some predictions with low support (but support anyway) can have AED score equal to 1? Or some purely abinitio prediction without support at all can anyway be selected even when keep_preds=0 is set up? </div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Jacques Dainat<br class="">
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