Gene direction in genomic scaffold

Joaquín de Navascués jdenavas at trasto.cbm.uam.es
Thu May 4 09:35:39 EST 2000


Hello.
I have recently begun using the genomic annotations showed by the NCBI.
Surprinsingly I found that the mRNAs and CDs within a scaffold are all
transcribed in the same direction if I believe the published
descriptions. I cannot think it is so.
So my question is: how could I know the orientation of a gene (predicted
or cloned) in a scaffold? Do I really need to type the CDs sequence as
described and translate it in the 6 frames to check if it is + or -?
I'd rather think there must be a better way. Do you know any?
Thanks a lot.
Joaquín de Navascués,
graduate student at the CBMSO, Spain.
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