how to find an overlap BAC

Sue Rhee rhee at acoma.Stanford.EDU
Thu May 18 14:39:33 EST 2000


Dear Karen,

TAIR's Sequence Table shows that the neighboring clone at the 5' end of
F18A17 is T14C9. This clone has been completely sequenced but not yet
annotated, as shown on TAIR's Sequence Map. If you click on the clone
names from either the Seq Table or Map, the full entry from AtDB's
database shows that both clones have been sequenced by Cold Spring Harbor
Lab. I used BLAST 2 Sequences with the accessions and did not find an
overlap, suggesting that there may be a gap.

You would be best off contacting Cold Spring Harbor Lab to find out more
information about this.

TAIR's Seq Table around F18A17:

	http://arabidopsis.org/cgi-bin/maps/Seqtable.pl?chr=5&beg=59&end=64

TAIR's Seq Map: (search for the clone name to get the view around the
clone)

	http://arabidopsis.org/cgi-bin/maps/Schrom

NCBI's BLAST 2 Sequences:

	http://www.ncbi.nlm.nih.gov/gorf/bl2.html

Cold Spring Harbor Lab's Arabidopsis website and contact info:

	http://nucleus.cshl.org/protarab/

Best,
Sue


On 18 May 2000, Karen S. Browning wrote:

>  I have located a gene of interest to me at the 5' end of BAC F18A17 from
>  chromosome 5.  The gene lies across the junction to the previous BAC
>  fragment.  I do not find the rest of the gene in the database.
>
>  I assume the BAC I need has not been sequenced yet.  Is there a way to find
>  out the status of the missing BAC?
>
>  Thank you!
>
>  Dr. Karen S. Browning
>  Assistant Professor
>  Department of Chemistry and Biochemistry
>  University of Texas
>  Austin, TX  78712
>
>  512-471-4562
>
>  512-471-8696 FAX
>
>  kbrowning at mail.utexas.edu
>
>  ---
>
>

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Sue Rhee                         	rhee at acoma.stanford.edu
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