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

[Tristan Fiedler]

Dear Bio Gurus!

Two quick questions :

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.

Currently each file looks similar to :

% cat -v seq_018_G05.seq
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA^M
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGG^M
TTTTTTTTTTTTTTTTCCCAAAAAAAAAAAAA^M


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


Thank you - and feel free to reply directly to me (not waste bb resources).

Cheers!



-- 
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)
305-361-4626