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what are survey sequences?

Mike Cherry cherry at genome.stanford.edu
Sat Nov 21 14:36:04 EST 1998


In general the Arabidopsis genomic survey sequences, those sequences
in GenBank's GSS section, are BAC end sequences.  BAC end sequences
are used in physical mapping and also as an aid to the genomic
sequencing groups.  Once a BAC has been sequenced it is then easy to
determine the neighboring BACs and how much overlap exists. This
allows the sequencing groups to appropriately select which neighboring
BAC to sequence.  These BAC end sequences are one pass sequences, like
ESTs, the reliability of the sequence is lower than genomic --
probably about 1% error.  Several groups have been generating the BAC
end sequences (TIGR, U. Penn, IGF, Genoscope) for a very large number
of BACs from the IGF and TAMU libraries.  An end sequence does not
mean that the specific BAC will be sequenced.  Of course, the whole
genome sequence is being determined and so the region represented by
an end sequence will be determined at some point.

Mike



>
> I have found several "genomic survey sequences" in the databases to genes
> that I am interested in.  What are these sequences and will the complete
> sequences be available soon?  Thanks for the information/education.
>
> 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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