EMBOSS on Michael’s Domain

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 `.

EMBOSS and GCK for the assembly and documentation of construct sequences

Thu, 05 Apr 2007 00:00:00 +0000

I am trying to use EMBOSS for the assembly of vector sequences. Long time ago, I used the CGC seqed program for this purpose and at the moment I use the Gene Construction Kit . EMBOSS doesn’t have a straight equivalent for seqed and one has to use a bunch of other tools to replace its functionality. Look at this comparison between CGC and EMBOSS .

Software development projects for Molecular Biology

Thu, 05 Apr 2007 00:00:00 +0000

GCK2.5-related

GCK2.5 debug under wine** There are still some bugs that make using gck2.5 sometimes a pain under wine. Especially the inability to annotate regions, to search for a sequence and to open a new file.
GCK2.5 export** GCK2.5 is not able to export in embl format with the regions converted into features. It can, however, export comments to text file and plain sequence to a text file. It should be trivial to write a perl script that takes these two files and converts them into one embl file, EMBOSS cirdna/lindna or pDRAW32 file.
GCK2.5/wine desktop integration** When clicking on files that are associated with Windows programs (using wine), the Linux file manager (e.g. Konqueror) passes the file as an argument to the associated Windows application and the file is opened under wine. However GCK2.5 refuses to accept the file as an argument. When clicking on a .gcc file, GCK2.5 starts up, but opens an empty window and I have to open the .gcc file from within GCK2.5. Unnecessary clicking, especially when I need to navigate over several folder hierachies. When GCK2.5 is running natively under Windows, is it possible to start GCK2.5 with a construct file as a command line argument? I should check that out.

pDRAW32-related

How to transfer the oligo database from MacVec tor to a web-based blast database

Tue, 06 Mar 2007 00:00:00 +0000

Save all sequences in one flatfile format (NOT MacVector format), e.g. genbank format.2. Copy all sequences to a Linux/UNIX computer and convert them from Mac format to UNIX format: mac2unix *.gb3. Write all sequence fiule names into one file: ls *.gb > oligo.lst4. Convert all sequences into one file of concatenated fasta entries using EMBOSS: seqret -sequence @oligo.lst -osformat fasta. Call the output file “mcbl_oligo_db"5. Put this fasta file into the blast web servers database directory (…/blast/db)6. Format the database: formatdb -i mcbl_oligo_db -p F -o T7. Edit …/blast/blast.html by adding the new database name8. Edit …/blast/blast.rc by adding the new database name

Shortcoming of silent mutagenesis tools (EMBOSS, GCK): WatCut as a solution

Sun, 22 Feb 2004 00:00:00 +0000

Update: As of May 2026, the last functional instance of the WatCut web service (by the University of Pittsburgh) was discontinued. However, tools like Snapgene ( https://snapgene.com ) have the same functionality (i.e. can detect novel restriction sites by silent mutagenesis of two nucleotides).