Bioinformatics on Michael’s Domain

The Staden package on Ubuntu for bioinformatics dinosaurs

Wed, 27 Jul 2016 00:00:00 +0000

Mostly we use the SnapGene software when we check the sequences of our DNA constructs. However, sometimes SnapGene’s alignment view is not flexible enough and then I fall back to using the ancient Staden Package . I just had upgraded from Ubuntu 14.04 to 16.04 and hence did not have Staden installed. I was pleasantly surprised when the installation of Staden took only about 15 seconds because finally - thanks to the Debian Med team - Staden is available from the universe repository (actually already since October 2014).sudo apt install stadenStaden is clearly not as intuitive as it could be, but it is very powerful and lends itself to automated processing of data. If you have the opportunity to learn it, I would encourage you to do so. The Finnish CSC recorded the Staden course from 2004, in which I participated and you can get the recordings from Funet TV . I just had briefly considered switching from Ubuntu to SuSE because of the ongoing wireless connection debacle that Canonical can’t seem to fix, but considering how non-trivial a manual install of Staden is, this is a big plus for Ubuntu. There are obviously dedicated Linux distributions for bioinformatics purposes, but they all tend to lag behind the latest and greatest developments of the major distros.

Python for Kids (and bioinformaticians)

Sat, 12 Mar 2016 00:00:00 +0000

I started to teach my son programming and we both are enjoying it. First we did a bit of html/php since he wanted to make an online quiz on his website, but now we started to work through the (German) book “Python für Kids” ( http://python4kids.net ). I chosen Python because it’s a modern, easy-to-read language, and nowadays probably the most popular first choice for starting programmers. It’s open source, easy to install on any system and you can get write powerful programs after a short learning period. Python for Kids uses the Turtle module, which enables a graphics-oriented introduction into programming. The graphics on the left is one of the results. Another very useful Python teaching resource for kids is Code Club .Python is also a very good choice for biologists and bioinformaticians, but since it is a multi-purpose language, you don’t limit yourself to certain tasks. There is Biopython , which is a very good toolset for the handling of DNA and protein sequences and even 3D structures.

Installing Staden 2003b on Suse 9

Thu, 24 May 2007 00:00:00 +0000

Download the sources .
cd into /usr/local and become su.
tar -xvzf /home/jeltsch/Documents/staden_linux_2003.0b1.tar.gz (jeltsch is my usename, thus has to be replaced for other users!!!!)

How to import sequences from SRS into GCK2.5

Wed, 23 May 2007 00:00:00 +0000

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.

Staden 1.4 and Suse 9

Mon, 21 May 2007 00:00:00 +0000

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.profilein 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)Apparently the usual file (/usr/lib/libstdc++.so.5) is not anymore used because the staden linux-binary directory is listed in the PATH variable in the very beginning and thus overrides all other entries. Thus I replaced /usr/local/staden-linux-rel-1-4/lib/linux-binaries/libstdc++.so.5 and libstdc++.so.5.0.1 by symbolic links to /usr/lib/libstdc++.so.5.0.5:cd /usr/local/staden-linux-rel-1-4/lib/linux-binariessudo ln -s /usr/lib/libstdc++.so.5.0.5 libstdc++.so.5.0.1sudo ln -s /usr/lib/libstdc++.so.5.0.5 libstdc++.so.5So far at least printing works without error messages, but I have not tried staden yet…

Automatization of Sequence Handling (Staden's pregap4 and gap4)

Sat, 19 May 2007 00:00:00 +0000

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.auxI put the script into ~/bin; and this script is supposed to be invoked from within the directory where the sequences are located. Typically the ab1 trace files from a single sequencing run from our machine are stored in one directory together with some (for me) meaningless log files, etc.First the script deletes unnecessary files from the directory; then it truncates filenames to 27 characters plus .ab1 ending. Funnily pregap4 handles longer filenames well, but gap4 has problems. Then all the remaining files are put into a list (tracefile.list) that is read by pregap4. pregap4 is used non-interactively. It gets its instructions (the setup of the modules) from a configuration file (which in my case is also stored in ~/bin).pregap4 calls the gap4 shotgun assembler and puts the readings into a gap4 database. Unfortunately I havn’t figured out how to automatically assign a descriptive name for this database. At the moment they will all have the same names and can be only identified based on their location in a different directory. It would be good to give them automatically a unique name, e.g. the date when the assembly was done or something similar.After all this has been done, gap4 is called and loads the newly created database for manual inspection and editing.Most of our sequencing is done to check newly made vectors. Therefore we usually know exactly what sequence we expect. If (which is unfortunately not the case) people use any program to document their constructs that included full sequence information (such as the Gene Construction Kit), the trace files should be automatically compared to such “expected” sequence.At the moment I achieve this by exporting the DNA sequence from the Gene Construction Kit program (GCK) as plain text file (apparently I could also use EMBL format) and putting this file together with the ab1 trace file into the same directory before starting the script. Thus it is handles just as any other sequence and the sequence readings are aligned to it.However, there are several things that I would like to be set automatically when invoking gap4 because I always perform the same sequence of clicks when manually inspecting in gap4 the alignment:Displaying all forward reading frames: I presume that because the “expected sequence” is the longest, it is always present in forward orientation in the assembly and the reading frames are allways forward. This results from the fact that I maintain (for ease of reading) the vector sequence in GCK allways in such orientation that the CDS of the GOI is in a forward frame.Highlighting disagreements by background color should be switched on.Upper/lower case character differences should be not handled as disagreementsBecause the quality of our sequencing is modest, mostly the default values are to strict for gap4 to enter the readings into the same contig. Thus I usually end up finding internal repeats and entering them manually. This should be possible to set automatically in the gap4 assembly, but I haven’t got around to figure out how.

kaptain on Suse Linux 9

Sat, 19 May 2007 00:00:00 +0000

I am currently trying out several graphical front ends for the molecular software package EMBOSS and I have read good reviews of kaptain . However, because there are no rpm packages of kaptain for Suse Linux 9 available, I tried to compile it myself. First problem was that the configure script couldn’t find the libraries and headers for qt3:> checking for Qt… configure: error: Qt (>= Qt 2.2.2) (headers and libraries) not found. Please check your installation!Thus I executed ./configure with the option:> ./configure --with-qt-dir=/usr/lib/qt3 Now the configuration script proceeds to the end. However, the make still fails, the last lines of output are like this:Making all in kaptain make[2]: Entering directory /home/jeltsch/downloads/kaptain-0.71/kaptain’ g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/lib/qt3/include -I/usr/X11R6/include -D_REENTRANT -O2 -fno-exceptions -fno-check-new -c kaptain.cpp kaptain.cpp: In constructor Kaptain::Kaptain(Intermediate*, Kaptain*, QWidget*, QBoxLayout*, QDialog*, bool, const char*)': kaptain.cpp:99: error: assert’ undeclared (first use this function) kaptain.cpp:99: error: (Each undeclared identifier is reported only once for each function it appears in.) kaptain.cpp: In member function void Kaptain::button_pressed()': kaptain.cpp:1576: error: ostream_iterator’ undeclared (first use this function) kaptain.cpp:1576: error: parse error before >' token kaptain.cpp:1598: error: parse error before >’ token make[2]: *** [kaptain.o] Error 1 make[2]: Leaving directory /home/jeltsch/downloads/kaptain-0.71/kaptain' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /home/jeltsch/downloads/kaptain-0.71’ make: *** [all-recursive-am] Error 2I got help from the author of the software Zsolt Terek. I had to insert at the beginning of kaptain.cpp:include include `.

Desktop Integration of Staden into KDE 3.2