[BiO BB] Poly A tail length - script help please

Tristan Fiedler tfiedler at rsmas.miami.edu
Tue Sep 9 17:00:55 EDT 2003

Thanks for the scripting tips!  I have a 'counting' issue which I need to
quickly resolve.  A typical sequence input file (5 - 700 bases) looks like


I have over 500 files, named *.seq.  I would like to create a script which :

a.  runs through all the files,
b.  counts the length of the 'poly A' tail (defined as the longest stretch
of A or N)
c. sends the output to a file, eg.

25 1.seq
87 2.seq
13 3.seq

Example valid poly A tails :





Thank you so much for your expertise!


Tristan J. Fiedler, Ph.D.
Postdoctoral Research Fellow
NIEHS Marine & Freshwater Biomedical Sciences Center
Rosenstiel School of Marine & Atmospheric Sciences
University of Miami

tfiedler at rsmas.miami.edu
t.fiedler at umiami.edu (alias)

More information about the BBB mailing list