[BiO BB] remove CTL-M and Buying a bioinformatics workstation

Philipp Pagel p.pagel at gsf.de
Thu Sep 4 02:51:50 EDT 2003

> 1.  could someone please assist me in writing a shell script (awk, sed,
> etc.) which would use a loop to run thru about 1000 files (filenames all
> end in '.seq') and remove all occurences of control-M, resulting in a file
> containing the sequence on a single line.

No script required. Just a one-liner...
cd into the folder with your sequences and do this:

for f in *.seq; do tr -d '\n' < $f > tmp_sequence; mv tmp_sequence $f; done

> 2.  We are planning to buy a workstation for our local (~3 labs producing
> sequences from an ABI sequencer) genomics needs (lots of blast runs,
> database management, standard bioinformatics software), and were planning
> on getting something like :
> 4 GB RAM  (is this enough for doing local blast searches against genbank?)
> 2 x 3 GHz Xeon processors (how about Mac OSX?)
> 400 GB storage

Sounds like a nice machine. Certainly big enough for BLAST.


Dr. Philipp Pagel                                Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS              Fax.  +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg, Germany

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