Andreas Wilm

Presentations

• Talk at the 3. RNA Workshop 2004 (Bielefeld, Germany).
  Title: "Construction of Consensus Structures == ConStruct"
• Poster from the RNA-Meeting 2004 (Blaubeuren, Germany).
  Title: "Benchmarking Structural RNA Alignment Programs"
• Poster from the Vienna RNA Meeting 2003 (Vienna, Austria).
  Title: "ConStruct: Enhanced RNA Structural Alignments and RNA Structure Prediction"
• Talk at the MPI-KG Golm 2004 (Potsdam, Germany).
  Title: "RNA Alignments and RNA Structure in silico"
• Presentation prepared for the Regulatory and functional RNAs meeting 2003 (Benasque, Spain).
  Title: "Using ConStruct"
• Poster from the RNA-Meeting 2002 (Blaubeuren, Germany).
  Title: "ConStruct: Thermodynamic Prediction of Conserved ssRNA's Structure"

Source

Debian Packages

Here you'll find some compiled Debian packages. Contact me if you need the corresponding orig.tar.gz, diffs or older versions. You may want to add
deb http://www.biophys.uni-duesseldorf.de/~wilm/deb/ /
to your sources.list.

biosquid

Squid is Sean Eddy's personal library of C functions and utility programs for sequence analysis. I had to call the package biosquid to avoid name clash with the proxy named squid.

• biosquid_1.9.g-1_i386.deb
• biosquid_1.9.g.orig.tar.gz

vienna-rna

Vienna RNA Secondary Structure Package

• vienna-rna_1.6-1_i386.deb
• vienna-rna_1.6-1.tar.gz

rna-forester

RNAforester: structural motif detection in RNA secondary structures based on local RNA structure alignments (as of version 1.6 part of vienna-rna!)

• rna-forester_1.4-1_i386.deb

Misc Sources

squicl

I really like Tcl/Tk but it lacks a BioPerl counterpart. That's why I created squicl, which provides an Tcl-interface to the Vienna RNA package (RNAfold etc.) and Squid routines. A command reference is currently missing, but example scripts are included. This version is known to work with vienna-rna 1.5b and squid 1.9g (local copies).

• squicl-0.3.0.tar.gz

maxbpmatch

During my Bioinformatics teaching courses I implemented Nussinov's algorithm for RNA folding via basepair maximization (dynamic programming) in several languages.
The C-source includes generic routines for handling stacks and matrices, including dotplots.
Compare this to the Perl version (html) and to the Tcl version (html).
A Bash version is still under construction ;).

Some test sets:

tRNA with bottom bulge

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tRNA with internal loop

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tRNA with top bulge

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tRNA with top bulge and unpaired nt in bifurcation

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Exits

• Institut für Physikalische Biologie (Department of Physical Biology)
• Heinrich-Heine University Düsseldorf
• A private homepage