[Bioperl-l] Restriction Enzymes
Roger Hall
Roger Hall" <roger@iosea.com
Wed, 22 Aug 2001 04:03:25 -0700
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I addressed a bug in the ::RestrictionEnzyme module based on an educated =
CS guess - and then I learned about restriction enzymes and their role =
in recombinant DNA technology.
Pretty cool stuff. ;}
The fix was an if/else switch to test the left and right limits of the =
sequence length, which avoids the interior assuming substring statement =
when either end-limit was given. (The interior statement assumed that =
there were two sections of sequence surronding the cleave mark '^'. At =
either end limit, there is no need to substring, and the attempt to grab =
some substring before the beginning or after the ending bombed.)
Please help me know that the data was correct (and the fix that =
followed): are there restriction enzymes that cleave at the beginning =
(or end) of the given sequence? My text book only shows four enzymes (at =
least in this chapter), and they all cleave at an interior position for =
the given sequence - but there are quite a few more than four enzymes =
initialized in ::RestrictionEnzyme!
Thanks!
Roger Hall
http://www.iosea.com/
650.201.7760
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<DIV><FONT face=3DArial size=3D2>I addressed a bug in the =
::RestrictionEnzyme module=20
based on an educated CS guess - and then I learned about restriction =
enzymes and=20
their role in recombinant DNA technology.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Pretty cool stuff. ;}</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>The fix was an if/else switch to test =
the left and=20
right limits of the sequence length, which avoids the interior =
assuming substring statement when either end-limit was given. (The =
interior=20
statement assumed that there were two sections of sequence surronding =
the cleave=20
mark '^'. At either end limit, there is no need to substring, and the =
attempt to=20
grab some substring before the beginning or after the ending=20
bombed.)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Please help me know that the data was =
correct (and=20
the fix that followed): are there restriction enzymes that cleave at the =
beginning (or end) of the given sequence? My text book only shows four =
enzymes=20
(at least in this chapter), and they all cleave at an interior position =
for the=20
given sequence - but there are quite a few more than four=20
enzymes initialized in ::RestrictionEnzyme!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thanks!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Roger Hall<BR><A=20
href=3D"http://www.iosea.com/">http://www.iosea.com/</A><BR>650.201.7760<=
/FONT></DIV></BODY></HTML>
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