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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>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>
<div><a href="http://www.uncc.edu">http://www.uncc.edu</a></div>
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