Protein Hypernetworks

Johannes Köster

This software will accompany our submitted "Protein Hypernetworks" paper once it is published.
The license is to be determined.
For access to our predictions, please see the Protein Hypernetworks research page.

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Motif Statistics and Discovery (MoSDi)

Tobias Marschall

The MoSDi software package contains several sequence analysis algorithms, including methods for

1. motif statistics, e.g. compute the exact occurrence count distribution of a motif,
2. exact motif discovery: extraction of motifs with provably optimal p-value,
3. analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text (see Research page).

Distributed under the GPL. Visit the MoSDi hompage for more details.

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Cutadapt: Remove adapter sequences from high-throughput sequencing reads

Marcel Martin
See the cutadapt Google code homepage.

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Horspool-Analyser (DEPRECATED, use MoSDi instead)

Tobias Marschall
This accompanies our LATA'10 paper (see Research): a JAVA program to compute the exact distribution of character accesses by Horspool's and Sunday's pattern matching algorithms. The code has been included into MoSDi (see above). However, you may still download this package to easily reproduce the results from our LATA'10 paper.
Source code: horspool-analysis-source.tar.gz

Distributed under the GPL.

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Further Software (not yet sorted)

• VerJInxer
• Promide / LOligoD
• REFORM
  
• HMM Logos
• Multinomial
  
• Parrondo Paradoxon
• StylePal