[Genome] BAC end pair orientation

[Terry Furey]

Mike -

For any given paired BAC end sequences, the left most end will always be 
on the + strand and the right most on the - strand.  This ensures the 
orientation of the end sequences are correct with respect to each other.

The orientation of the whole BAC is determined by whether the right most 
end sequence is from the 5' or the 3' end of the BAC.  If it is the 5' BAC 
end sequence, then the BAC is from the + genomic strand, and if it is the 
3' BAC end sequence, the BAC is from the - genomic strand.

Terry

On Tue, 11 Jul 2006, Mike Mitchell wrote:

> How do you determine the orientation of a BAC end pair on the genome?
>
> For example, RP23-21K22 is mapped to the reverse strand of of mouse
> chr17:30686715-30907042 (mm8 / NCBI 36), but the left most end (AZ104124) is
> on the + strand and the right most end (AZ104126) is on the - strand.
>
> I am attempting to determine which BACs would be the most useful to order
> from the CHORI BAC&PAC repository, and was hoping to select BACs with my
> gene of interest on the same relative strand as on the genome.
>

----------------------------------------------------------------
Terrence S. Furey
Scholar, Institute for Genome Sciences and Policy (IGSP)
Assistant Research Professor
Dept of Biostatistics and Bioinformatics
Dept of Computer Science
Duke University
101 Science Dr, Box 3382
Durham, NC 27708
Phone: 919-668-4728
Fax: 919-668-0795