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We have found that many apparent problems with tools in PopGenIE can result from previous results that have been cached. Before reporting a bug/problem we would request that you first clear your browser cache, quit the browser, again clear the cache when you re-open the browser and then finally check that the problems remains.
How can I convert Populus trichocarpa version 1 gene ids into version 2 gene ids?
Please go to http://v2.popgenie.org/flashbulktools and choose the ID conversion option. Then select the Populus Genome from dropd down menu. Finally paste your old gene ids and click GO button.
How can I convert Populus trichocarpa version 2 gene ids into version 3 gene ids?
Please go to Gene Search tool and paste your old gene ids.
How can I download all protein/nucleotide sequences from my active gene list?
Please use the Sequence Search tool, which is listed in the Analysis section. In there you can select P. trichocarpa peptide/nucleotide, click on the search button and then on the download button. You will then have a FASTA file of the protein/nucleotide sequences for the genes in your active gene list.
Where can I find PU sequences?
You can find the PU sequences as well as corresponding BEST blast homologous in this directory (ftp://plantgenie.org/Data/PopGenIE/Populus_trichocarpa/v3.0/v10.1/Annotation/id_conversion/).