Balazs, Another source of human BAC information is provided by the NCBI CloneRegistry. This is an old database from the original draft sequencing of the human genome and mostly contains clone data available 10 years ago. Anyhow, I took a quick look at the registry and it reveals that this BAC has been end-sequenced (but only for one end; the other end was likely attempted but had failed to generate acceptable data). See: http://www.ncbi.nlm.nih.gov/nucgss/3348315?dopt=genbank
Obviously, you cannot "precisely" align a BAC clone with the human assembly with only one end-sequence. However, you can use this sequence in combination with the UCSC Blat program to map the location and orientation of the end-sequence. A reasonable hypothesis of the map position would then be a genomic fragment of approximately 180,000 bp starting from the aligned end-sequence (180 kb is the average insert size for the RP11 BAC library). In any case, one end or both ends available, it will never generate a precisely mapped BAC. In about 10% of the cases, sample- and data-tracking errors connect the wrong clone name with the data. Please realize that BAc-end sequencing was at its infancy and sequencing was not done at the time on capillary machines but on ABI slab gels, and DNA preps were not isolated in 96-well format. Pieter de Jong -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Vanessa Kirkup Swing Sent: Thursday, September 16, 2010 10:43 AM To: Balazs Nemeti Cc: genome Subject: Re: [Genome] BAC location Dear Balazs, It appears that we don't have the identifier in our our database. By doing a google search using that identifier I was able to find this: http://cancer.ucsf.edu/_docs/cores/array/analysis/HA32K_B.clonepos.20050919. txt Hopefully this gives you the information that you need. Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Balazs Nemeti" <[email protected]> To: "genome" <[email protected]> Sent: Thursday, September 16, 2010 12:52:29 AM GMT -08:00 US/Canada Pacific Subject: [Genome] BAC location Dear Madam/Sir, I encountered a problem I cannot resolve. I have a BAC clone for which I am not able to retrieve its exact chromosomal location. Its identifier is: RP11-51K21. I have already tried via ucsc.edu Table browser, which helped me a lot to find the location of many of my BAC clones. I have tried NIH website as well. I would appreciate if you could provide me with the location of the BAC mentioned above. Thank you for the efforts. Wishing the best, Balazs Nemeti. _______________________________________________ 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
