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<div>Sorry to bother you!</div>
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<div>I didn't realize that MSU has already annotated the genes in MSU7 using GOSlim terms, which I think will meet my needs:</div>
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<div><a href="ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.GOSlim_assignment">ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.GOSlim_assignment</a></div>
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<div>I got the file from them and am using it that one for now.</div>
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<div>Thank you and I hope all is well despite the hurricane. </div>
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<div>Best,</div>
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<div>Ann</div>
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<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri">-------------------------------</font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri">Ann Loraine, Ph.D.</font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Associate Professor</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Department of Bioinformatics and Genomics</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">University of North Carolina at Charlotte</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">North Carolina Research Campus</span></font></font></div>
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<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Kannapolis, NC 28081</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">704-250-5750</span></font></font></div>
<div>aloraine@uncc.edu</div>
<div><a href="http://www.transvar.org">http://www.transvar.org</a></div>
<div><a href="http://www.bioviz.org">http://www.bioviz.org</a></div>
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<span style="font-weight:bold">From: </span>Ann Loraine <<a href="mailto:aloraine@uncc.edu">aloraine@uncc.edu</a>><br>
<span style="font-weight:bold">Date: </span>Sun, 28 Oct 2012 18:42:56 -0400<br>
<span style="font-weight:bold">To: </span><<a href="mailto:gramene@gramene.org">gramene@gramene.org</a>><br>
<span style="font-weight:bold">Subject: </span>GO analysis of RNA-Seq data<br>
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<div>Hello,</div>
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<div>I am using GOSeq (Bioconductor package) to analyze some RNA-Seq data from rice. </div>
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<div>I'm writing to ask your advice on how to best use the rice GO annotations Gramene has provided on the geneontology.org Web site.</div>
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<div>I have differential expression information for genes annotated as part of the (latest) MSU7 gene annotations release.</div>
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<div>(I made it by aligning my reads against the assembly. I then counted reads that overlapped the MSU7-annotated gene models.)</div>
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<div>However, it is not entirely clear how to map rice genome locus ids (such as LOC_Os06g31210) onto the Gene Ontology category annotations listed in the gene association file (gene_association.gramene_oryza.gz) available from geneontology.org.</div>
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<div>I see that some of the lines contain ids such as LOC_Os06g31210, which look like gene ids from the MSU annotations.</div>
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<div>My question is: can you explain how I should map MSU7 locus ids onto the GO ids listed in the file?</div>
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<div>It looks like you were using the Uniprot id as the primary key. If I could get a mapping between Uniprot id and MSU7 locus identifiers, that would probably be enough.</div>
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<div>Could you let me know what the best way to do this would be? </div>
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<div>I can easily run blast, blat, or write a simple program to match fields across files. For example, I could extract the genomic sequence for each gene model and then use blastx to identify the best hit protein id from SwissProt/UniProt. If the GO file is
using the Uniprot id as the primary key, then I could link locus ids to GO terms using the best hit from Uniprot. </div>
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<div>Does this sound like it would work or would you recommend a more straightforward path?</div>
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<div>Thank you so much for the Gramene resource and for providing the GO annotations!</div>
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<div>Best wishes,</div>
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<div>Ann Loraine</div>
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<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri">-------------------------------</font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Ann Loraine, Ph.D.</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Associate Professor</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Department of Bioinformatics and Genomics</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">University of North Carolina at Charlotte</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">North Carolina Research Campus</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">600 Laureate Way</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">Kannapolis, NC 28081</span></font></font></div>
<div><font class="Apple-style-span" color="rgb(0, 0, 0)"><font class="Apple-style-span" face="Calibri"><span class="Apple-style-span" style="font-size: 14px;">704-250-5750</span></font></font></div>
<div><a href="mailto:aloraine@uncc.edu">aloraine@uncc.edu</a></div>
<div><a href="http://www.transvar.org">http://www.transvar.org</a></div>
<div><a href="http://www.bioviz.org">http://www.bioviz.org</a></div>
<div><a href="http://www.uncc.edu">http://www.uncc.edu</a></div>
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