The Sequence Analysis Department offers a number of professional sequence analysis tools to the bioinformatics research community. They were developed and are maintained by our group and our collaborators.

Currently, the following tools are available:

• AGenDA - Alignment-based Gene Detection Algorithm
  

  AGenDAGene prediction by cross-species sequence comparison.

• AltAVisT - Alternative Alignment Visualization Tool
  

  AltAVisTCompares two alternative multiple alignments of the same sequence familiy; regions where both alignments coincide are highlighted.

• DCA - Divide and Conquer Multiple Sequence Alignment
  

  Divide-and-Conquer Multiple Sequence Alignment (DCA) is a very fast sequence alignment algorithm producing high quality alignments (close to the optimal alignment under the sum-of-pairs score).

• DIALIGN
  

  DIALIGN is a novel alignment program based on segment-to-segment comparison. It is especially suited to detect local similarities among distantly related sequences.

• GeneFisher

  GeneFisher is a software tool for selection of primers for the polymerase chain reaction (PCR). It goes beyond other available tools by designing degenerate primers for an unknown target from a family of homologue sequences.

• JALI

  Jumping Alignments Jali is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.

• MFold - Prediction of RNA Secondary Structure by Energy Minimization

  MFold is a set of programs developed by M. Zuker and the laboratory of D.H. Turner that uses dynamic programming to predict RNA secondary structures by free energy minimization.

• MGA - Multiple Genome Aligner

  MGA The software tool MGA efficiently computes multiple genome alignments of large, closely related DNA sequences.

• paRNAss - Prediction of Alternative RNA Secondary Structures

  paRNAss is a software tool aiming to predict conformational switching in RNA.

• REPuter - Fast Computation of Maximal Repeats in Complete Genomes

  REPuter computes all maximal duplications and reverse, complemented and reverse complemented repeats in a DNA input sequence.

• RIFLE - Rapid Identification by Fragment Length Evaluation

  RIFLE is a tool for the fast, 16S rDNA-based identification of microorganisms without sequencing.

• RNA Movies

  RNA Movies is a system for the visualization of RNA secondary structure landscapes. Its input is a script consisting of structures from which animated graphical structure representations are generated. In this way, it creates the impression of an RNA-molecule moving through its own 2D structure space.

• ROSE - Random-model Of Sequence Evolution

  Rose implements a new probabilistic model of RNA-, DNA-, or protein-sequence evolution.

• SplitsTree

  SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences.

• TSDA - target site duplication align

  TSDA(target site duplication align) is an alignment tool to analyse recombinant DNA sequences. The program calculates (local) similarity of two sequences and shows the optimal alignment(s). The development was done using the algebraic dynamic programming (ADP) method.

• WOTD

  WOTD Wotd is an implementation of the "lazy" write-only top-down construction algorithm of suffix trees using a very space-efficient representation.