zhenqing ye wrote: >For example HgaI GACGC (5/10) indicates cleavage as >follows: > 5' GACGCNNNNN^ 3' > 3' CTGCGNNNNNNNNNN^ 5' >it should be 5'-overhang according to biological rule, but >in the code implementation it's 3'-overhang. i think the >defination of overhang in the code implementation >is related with the strand direction.
It's a 5'overhang and if biojava says otherwise, it is most probably a bug. It is just confusing because we use the word "end" to describe both the enzyme cuts (end type using biojava javadoc terminology) and the strand termini (termination of a strand either 3' end or 5' end). - George _______________________________________________ Biojava-l mailing list - [email protected] http://biojava.org/mailman/listinfo/biojava-l
