Question: BioConductor beginner needing to annotate clones
15.9 years ago by
Law, Annie • 70
Law, Annie • 70 wrote:
Hi, I am new to BioConductor and would appreciate advice with the following. My goal is to take cloneID's from for example Human microarray 19K human ESTs and find out the corresponding accession number and subsequently Unigene identifier. I would like to keep a database of this information. I would also like to know if a cloneID has changed and if so note this is the database and also update any corresponding information. I would like to know what the best way is to proceed with this. I have looked at the vignettes and it seems that the AnnBuilder package should be used instead of the annotate package? I went to the I.M.A.G.E. consortium and found out that they have an ftp site where I can download a file including information for all clones including IMAGE cloneID and Genbank accession numbers among other fields. My first goal in this project would be able to compare my list of cloneIDs to the file available on the I.M.A.G.E. consortium ftp site. However, I don't think that I can use the ABPkgBuilder since it requires a text file with two columns and the I.M.A.G.E. consortium site is not one of the accepted sites for the ABPkgBuilder. Any suggestions? If somehow I do get the list of my cloneIDs and corresponding accession numbers I think I will be able to use the ABPkgBuilder. Is this true? Also where can I look for information on dumping results form AnnBuilder into a database? Are there tracking tools within BioConductor, AnnBuilder? For example, is there a tracking tool available to let you know if a cloneID has changed? what is the best way to create a user friendly interface with BioConductor? Is there a GUI interface tool available in the BioConductor package? If not I may think of creating my own web interface or dumping the information from the data base on an Excel sheet. thanks very much for your help, Annie.
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