bioinformatics

Obviously you can import sequences into GCK2.5 directly from Genbank. But usually you are working with a web tool like SRS and end up having your sequences displayed in your browser. From SRS version 7 the import goes as follows: From your fancy display, click SAVE. From the pull-down menu "Use view" select * Complete Entries *. Then "Output to" FILE (TEXT). Check under "Save as type" SAVE TABEL AS ASCii TABLE/TEXT WITH. Click SAVE and save it somewhere with the file extension .ebl. Then from within GCK2.5 select IMPORT and select the file. Ready.

I installed today the new Staden package (version 1.4) to my Suse 9. I included the lines:

export STADENROOT=/usr/local/staden-linux-rel-1-4 . $STADENROOT/staden.profile

in my ~/.bashrc file.
After this kprinter broke with the following error:

kprinter: /usr/local/staden-linux-rel-1-4/lib/linux-binaries/libstdc++.so.5: no version information available (required by /opt/kde3/lib/kprinter.so)

Already a while ago I wrote a script, that tries to automatize most of the work involved in getting sequences from our ABI sequencer into a gap4 database. The script is far from perfect and looks like this:

!/bin/sh rm *.seq *.log Log\ file.txt for i in `ls *.ab1`; do echo "Renaming $i" mv $i `echo $i | sed "s/\(.\{27\}\).*/\1\.ab1/"` done ls *.ab1 *.txt > tracefile.list pregap4 -nowin -config /home/jeltsch/bin/pregap4_gap4.conf -fofn tracefile.list gap4 test.0.aux