DynaClip: An End-Clipping Program for the Mac

Jared Roach roach at u.washington.edu
Fri Sep 13 03:36:36 EST 1996


	As if we needed another one, right?
	
	However, I have found it very useful, as have others in my 
lab, so I felt it would only be fair to share it with everyone.

	So here's the help text from DynaClip, which should speak 
for itself:

     DynaClip is a program designed to trim a little bit off 
of the 5' and 3' ends of DNA sequence reads.  These will be 
simple text files - no returns - no spaces - no GCG format or 
anything.  The ".Seq" files produced by an ABI automated DNA 
sequencer are a fine example of what I'm talking about here.
    Now DynaClip is a fine program and will do a nice job.  
But, if you are an idealist, you will only mask regions of 
your sequence that don't interest you, and save everything 
else.  End-clipping is retro, and should be considered a 
throwback to the past.  However, sometimes the future is a 
little slow to arrive and be universally implemented.  We 
find DynaClip tremendously useful to munch our cDNA sequences 
before we search them against a database.  We find that 
SearchLauncher is an excellent downstream application from 
DynaClip.  And then HTTP_Directory_Maker is useful to catalog 
the SearchLauncher output.  Enjoy.
     Probably the nicest thing about DynaClip is that it does 
an almost perfect job of getting rid of the portion (hopefully 
its just a portion) of your sequence that is vector sequence.  
If you have a really short insert, it will get rid of your vector 
both 5' and 3'.  SInce it uses dynamic alignment, this end 
clipping works even if the cloning site is missing (i.e. chewed 
back or the like) or was compressed (a common cloning site occurence).
     DynaClip also produces a nice output so you can see your 
clipping statistics.
     DynaClip ships with the Strategene lambda-ZAP cloning 
site sequences - if you're using another vector, you'll have 
to input the sequences appropriate to your vector.
     DynaClip does not mask regions of low complexity.  I don't 
even know the right algorithm to use to do that.

You can find DynaClip at:

http://weber.u.washington.edu/~roach/Programs/

Hopefully, someone will find it useful.


------------------------------------------------------------------
Jared C. Roach
Department of Molecular Biotechnology
Health Sciences Building, Room K354
University of Washington
Box 357730
Seattle, WA 98195
phone  (206) 616-4536
FAX    (206) 685-7301
roach at u.washington.edu
http://weber.u.washington.edu/~roach/





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