<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="">You can set always_complete=1 for MAKER tottery and fix partial models (it walks out on both sides looking for canonical stops/starts). Also to clean up partial models and other submission issues, try using Comparative Annotation Toolkit (CAT). It will take MAEKR results and do all the NCBI related corrections automatically. It makes submission so much easier.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 1, 2020, at 12:31 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">I ran my annotation using ESTs from NCBI and transcriptome data and Swiss-prot data. I used SNAP trained twice after which Augustus was trained once.<div class=""><br class=""></div><div class="">I tried to submit the annotated genome to NCBI but have some problems I have not experienced before and do not know how to solve.</div><div class=""><br class=""></div><div class="">Some of the CDS features have invalid translations. Every CDS feature should have a valid start and stop codon, and should not have any internal stops. The only exception is if the CDS is partial at the end of a sequence or at an intron/exon boundary. If the CDS is partial, it must have the appropriate partial symbols. <br class=""><br class="">If a CDS feature does not have a valid translation (for example if there is a frameshift), please remove the CDS feature and annotate this with a single gene feature across the entire span. Include a note on the gene with a brief description. For example:<br class=""><br class="">1 200 gene<br class=""> gene phoA<br class=""> gene_desc alkaline phosphatase<br class=""> locus_tag OBB_0001<br class=""> note nonfunctional due to frameshift<br class=""><br class="">[3] There are 1075 gene features that are not associated with<br class="">any other features (CDS, rRNA, etc.) and are not labelled as<br class="">pseudogenes or as nonfunctional genes. Did you lose some of<br class="">the annotation you intended to include.<br class=""></div><div class=""><br class=""></div><div class="">Please how can this be solved?</div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel,Ph.D<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">+2348068124819</div><div class="">Publications: </div><div class=""> <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div></div></div></div></div></div>
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