Hi Yvonne, I presume your question indicates that 1)you want to select one or more BAC clones for a gene of interest, and 2)retrieve the sequences for these selected BAC clones. You might want to take a look at the Q&A section of the BACPAC Resources website.
The answer to the BAC selection is explained in the BACPAC answer to question #10. This answer explains the search for appropriate (mouse) BAC clones using either the UCSF Browser or the NCBI CloneFinder program. http://bacpac.chori.org/FAQ2.htm For the retrieval of sequences, you may be out of luck for most BAC clones: most BAC clones have only been sequenced for the BAC-ends. There are different procedures to follow for finding BAC-end sequences versus whole-insert BAC sequences. The BACs which are only end-sequenced are usually well displayed in the UCSC Genome Browser (if you activate the "BAC End Pairs" menu to the "Full" option). The reference mouse genome was derived from the C57BL/6J strain and the mouse RP23 and RP24 BACs are from the same strain. Hence, if you know the precise end-points of the BACs (defined by the aligned BAC-ends), then you can retrieve the corresponding reference sequence using the "DNA" button on the UCS Browser and then use the correct nucleotide start- and end-positions for the BAC-defined region. Retrieval of the actual sequences obtained experimentally is a bit more challenging and requires the access to the soon to disappear NCBI Trace Archive (for the actual BAC-end sequences). Clones which have been sequenced completely (for the mouse genome), are usually displayed in the UCSC Browser by their NCBI accession numbers and not by clone ID. You will only see these, if you have activated the "Assembly" menu for the browser, preferably by the "Full" option. Please realize that the actual BAC may have more sequence than is displayed or present in the NCBI Accession file. For most assemblies, only the "finished" sequence is maintained and displayed. If two "shotgun-sequenced" BAC clones overlap, the overlap region is only "finished" for one of the BAC clones. Hence, please, be aware that the BAC may contain more sequence than displayed. Pieter de Jong -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Luvina Guruvadoo Sent: Friday, April 08, 2011 10:43 AM To: Yvonne Fondufe-Mittendorf Cc: [email protected] Subject: Re: [Genome] bac sequences Hi Yvonne, Please see this previously answered question for instructions on how to retrieve BAC clone sequences: https://lists.soe.ucsc.edu/pipermail/genome/2005-March/006994.html Feel free to contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Yvonne Fondufe-Mittendorf wrote: > Hi, > I would like to order BAC clones and would like to know the sequences. How do I > get the sequences? > Thanks yvonne. > > Yvonne Fondufe-Mittendorf, Ph.D. > Assistant Professor > Department of Molecular and Cellular Biochemistry > University of Kentucky > BBSRB Room 273 > Lexington KY 40536-0509 > Office: 859.323.0091 > Fax: 859.323.5505 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
